R/get_mutations_read_names.R
get_mutations_read_names.RdThis function extracts the names of the reads in a bam file that support the variant and reference alleles of the input mutations
get_mutations_read_names(bam, mutations, min_base_quality = 20, tag = "", min_mapq = 30)
| bam | path to bam file |
|---|---|
| mutations | A data frame containing the mutations. Must have the columns CHROM, POS, REF, ALT. |
| min_base_quality | integer specifying the minimum base quality for reads to be included. |
| tag | the RG tag if the bam has more than one sample |
| min_mapq | integer specifying the minimum mapping quality for reads to be included |
A list with length equal to the number of mutations. Each element is a character vector with the read names.
Returns the IDs of the read that cover the input mutations (ref and alt alleles).
get_mutations_read_counts get_mutations_fragment_size test_ctDNA
data("mutations", package = "ctDNAtools") bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools") get_mutations_read_names(bam = bamT1, mutations = mutations[1:3, ])#> $`chr14:106327474_C_G` #> $`chr14:106327474_C_G`$ref #> [1] "T1_Library1:1954851" "T1_Library1:1955625" "T1_Library1:1956206" #> [4] "T1_Library1:1956604" "T1_Library1:1956608" "T1_Library1:1956615" #> [7] "T1_Library1:1956618" "T1_Library1:1956313" "T1_Library1:1956619" #> [10] "T1_Library1:1954604" "T1_Library1:1956103" "T1_Library1:1956157" #> [13] "T1_Library1:1956626" "T1_Library1:1956167" "T1_Library1:1956628" #> [16] "T1_Library1:1956631" "T1_Library1:1956081" "T1_Library1:1956186" #> [19] "T1_Library1:1956634" "T1_Library1:1956138" "T1_Library1:1956170" #> [22] "T1_Library1:1956368" "T1_Library1:1956637" "T1_Library1:1956639" #> [25] "T1_Library1:1956640" "T1_Library1:1956641" "T1_Library1:1956643" #> [28] "T1_Library1:1956644" "T1_Library1:1956646" "T1_Library1:1956649" #> [31] "T1_Library1:1956650" "T1_Library1:1956651" "T1_Library1:1956655" #> [34] "T1_Library1:1956662" "T1_Library1:1956664" "T1_Library1:1956666" #> [37] "T1_Library1:1954235" "T1_Library1:1954993" "T1_Library1:1955012" #> [40] "T1_Library1:1955454" "T1_Library1:1955614" "T1_Library1:1956132" #> [43] "T1_Library1:1956141" "T1_Library1:1956142" "T1_Library1:1956158" #> [46] "T1_Library1:1956244" "T1_Library1:1956246" "T1_Library1:1956667" #> [49] "T1_Library1:1956668" "T1_Library1:1956669" "T1_Library1:1956670" #> [52] "T1_Library1:1956672" "T1_Library1:1956677" "T1_Library1:1956679" #> [55] "T1_Library1:1956680" "T1_Library1:1956686" "T1_Library1:1956687" #> [58] "T1_Library1:1956688" "T1_Library1:1956694" "T1_Library1:1956695" #> [61] "T1_Library1:1956696" "T1_Library1:1956698" "T1_Library1:1956701" #> [64] "T1_Library1:1956703" "T1_Library1:1956715" "T1_Library1:1956716" #> [67] "T1_Library1:1954887" "T1_Library1:1956150" "T1_Library1:1956718" #> [70] "T1_Library1:1956719" "T1_Library1:1956155" "T1_Library1:1956720" #> [73] "T1_Library1:1954822" "T1_Library1:1956727" "T1_Library1:1956731" #> [76] "T1_Library1:1955221" "T1_Library1:1956109" "T1_Library1:1956110" #> [79] "T1_Library1:1956121" "T1_Library1:1956127" "T1_Library1:1956218" #> [82] "T1_Library1:1956743" "T1_Library1:1955222" "T1_Library1:1956152" #> [85] "T1_Library1:1956153" "T1_Library1:1956159" "T1_Library1:1956211" #> [88] "T1_Library1:1956372" "T1_Library1:1956373" "T1_Library1:1956746" #> [91] "T1_Library1:1956749" "T1_Library1:1956751" "T1_Library1:1956755" #> [94] "T1_Library1:1956188" "T1_Library1:1956757" "T1_Library1:1956123" #> [97] "T1_Library1:1956760" "T1_Library1:1956762" "T1_Library1:1956766" #> [100] "T1_Library1:1956768" "T1_Library1:1956773" "T1_Library1:1956212" #> [103] "T1_Library1:1956249" "T1_Library1:1956250" "T1_Library1:1956780" #> [106] "T1_Library1:1956784" "T1_Library1:1956786" "T1_Library1:1956788" #> [109] "T1_Library1:1956796" "T1_Library1:1956798" "T1_Library1:1956804" #> [112] "T1_Library1:1956805" "T1_Library1:1956806" "T1_Library1:1956807" #> [115] "T1_Library1:1956810" "T1_Library1:1956814" "T1_Library1:1956819" #> [118] "T1_Library1:1956822" "T1_Library1:1956823" "T1_Library1:1956825" #> [121] "T1_Library1:1956829" "T1_Library1:1956831" "T1_Library1:1956836" #> [124] "T1_Library1:1956307" "T1_Library1:1956846" "T1_Library1:1956848" #> [127] "T1_Library1:1956028" "T1_Library1:1956129" "T1_Library1:1956191" #> [130] "T1_Library1:1956194" "T1_Library1:1956857" "T1_Library1:1955876" #> [133] "T1_Library1:1956862" "T1_Library1:1956866" "T1_Library1:1956868" #> [136] "T1_Library1:1956871" "T1_Library1:1956875" "T1_Library1:1956878" #> [139] "T1_Library1:1956879" "T1_Library1:1956880" "T1_Library1:1956881" #> [142] "T1_Library1:1954624" "T1_Library1:1956229" "T1_Library1:1956336" #> [145] "T1_Library1:1955509" "T1_Library1:1956292" "T1_Library1:1956252" #> [148] "T1_Library1:1956311" "T1_Library1:1956891" "T1_Library1:1956894" #> [151] "T1_Library1:1956255" "T1_Library1:1956896" "T1_Library1:1956897" #> [154] "T1_Library1:1956900" "T1_Library1:1956906" "T1_Library1:1956907" #> [157] "T1_Library1:1955748" "T1_Library1:1956910" "T1_Library1:1956911" #> [160] "T1_Library1:1956916" "T1_Library1:1956917" "T1_Library1:1956918" #> [163] "T1_Library1:1956922" "T1_Library1:1956924" "T1_Library1:1956926" #> [166] "T1_Library1:1956927" "T1_Library1:1956930" "T1_Library1:1956931" #> [169] "T1_Library1:1956937" "T1_Library1:1956940" "T1_Library1:1956941" #> [172] "T1_Library1:1956945" "T1_Library1:1952419" "T1_Library1:1956331" #> [175] "T1_Library1:1956400" "T1_Library1:1956448" "T1_Library1:1956469" #> [178] "T1_Library1:1956958" "T1_Library1:1955049" "T1_Library1:1956375" #> [181] "T1_Library1:1956483" "T1_Library1:1956144" "T1_Library1:1956178" #> [184] "T1_Library1:1956356" "T1_Library1:1956485" "T1_Library1:1956965" #> [187] "T1_Library1:1956261" "T1_Library1:1956435" "T1_Library1:1956966" #> [190] "T1_Library1:1956967" "T1_Library1:1955366" "T1_Library1:1956317" #> [193] "T1_Library1:1956977" "T1_Library1:1956978" "T1_Library1:1956263" #> [196] "T1_Library1:1956538" "T1_Library1:1956982" "T1_Library1:1956989" #> [199] "T1_Library1:1956990" "T1_Library1:1956992" "T1_Library1:1955056" #> [202] "T1_Library1:1956226" "T1_Library1:1956402" "T1_Library1:1956057" #> [205] "T1_Library1:1953783" "T1_Library1:1955615" "T1_Library1:1956267" #> [208] "T1_Library1:1956269" "T1_Library1:1956299" "T1_Library1:1956344" #> [211] "T1_Library1:1956363" "T1_Library1:1956394" "T1_Library1:1956432" #> [214] "T1_Library1:1956471" "T1_Library1:1956519" "T1_Library1:1956520" #> [217] "T1_Library1:1956539" "T1_Library1:1956558" "T1_Library1:1957011" #> [220] "T1_Library1:1957013" "T1_Library1:1957014" "T1_Library1:1957016" #> [223] "T1_Library1:1957022" "T1_Library1:1957024" "T1_Library1:1957030" #> [226] "T1_Library1:1957031" "T1_Library1:1957035" "T1_Library1:1957039" #> [229] "T1_Library1:1957040" "T1_Library1:1957046" "T1_Library1:1957047" #> [232] "T1_Library1:1957048" "T1_Library1:1956233" "T1_Library1:1956339" #> [235] "T1_Library1:1957050" "T1_Library1:1957052" "T1_Library1:1956380" #> [238] "T1_Library1:1957054" "T1_Library1:1957055" "T1_Library1:1956403" #> [241] "T1_Library1:1957060" "T1_Library1:1957061" "T1_Library1:1955229" #> [244] "T1_Library1:1955728" "T1_Library1:1955843" "T1_Library1:1956272" #> [247] "T1_Library1:1956293" "T1_Library1:1956321" "T1_Library1:1956437" #> [250] "T1_Library1:1956445" "T1_Library1:1956456" "T1_Library1:1956541" #> [253] "T1_Library1:1956559" "T1_Library1:1957065" "T1_Library1:1955480" #> [256] "T1_Library1:1956581" "T1_Library1:1956582" "T1_Library1:1957067" #> [259] "T1_Library1:1957076" "T1_Library1:1957077" "T1_Library1:1957079" #> [262] "T1_Library1:1957080" "T1_Library1:1957084" "T1_Library1:1957087" #> [265] "T1_Library1:1957092" "T1_Library1:1955026" "T1_Library1:1956439" #> [268] "T1_Library1:1956525" "T1_Library1:1956562" "T1_Library1:1957093" #> [271] "T1_Library1:1957094" "T1_Library1:1957097" "T1_Library1:1957099" #> [274] "T1_Library1:1956413" "T1_Library1:1956502" "T1_Library1:1957102" #> [277] "T1_Library1:1957104" "T1_Library1:1957105" "T1_Library1:1957106" #> [280] "T1_Library1:1957107" "T1_Library1:1955230" "T1_Library1:1956405" #> [283] "T1_Library1:1956415" "T1_Library1:1956477" "T1_Library1:1954863" #> [286] "T1_Library1:1956199" "T1_Library1:1957117" "T1_Library1:1957124" #> [289] "T1_Library1:1957125" "T1_Library1:1955729" "T1_Library1:1955645" #> [292] "T1_Library1:1957130" "T1_Library1:1957132" "T1_Library1:1957136" #> [295] "T1_Library1:1957137" "T1_Library1:1957140" "T1_Library1:1957141" #> [298] "T1_Library1:1957145" "T1_Library1:1957147" "T1_Library1:1957148" #> [301] "T1_Library1:1955590" "T1_Library1:1957152" "T1_Library1:1957153" #> [304] "T1_Library1:1955923" "T1_Library1:1956029" "T1_Library1:1956030" #> [307] "T1_Library1:1956113" "T1_Library1:1956365" "T1_Library1:1957157" #> [310] "T1_Library1:1957159" "T1_Library1:1957160" "T1_Library1:1957161" #> [313] "T1_Library1:1957165" "T1_Library1:1957166" "T1_Library1:1957167" #> [316] "T1_Library1:1957168" "T1_Library1:1956564" "T1_Library1:1957172" #> [319] "T1_Library1:1957174" "T1_Library1:1955485" "T1_Library1:1955845" #> [322] "T1_Library1:1956440" "T1_Library1:1956452" "T1_Library1:1956458" #> [325] "T1_Library1:1956276" "T1_Library1:1956490" "T1_Library1:1957177" #> [328] "T1_Library1:1957179" "T1_Library1:1957182" "T1_Library1:1955791" #> [331] "T1_Library1:1957185" "T1_Library1:1956527" "T1_Library1:1957190" #> [334] "T1_Library1:1957198" "T1_Library1:1957199" "T1_Library1:1957200" #> [337] "T1_Library1:1956419" "T1_Library1:1957201" "T1_Library1:1955413" #> [340] "T1_Library1:1956360" "T1_Library1:1953517" "T1_Library1:1955913" #> [343] "T1_Library1:1956517" "T1_Library1:1955977" "T1_Library1:1956077" #> [346] "T1_Library1:1956522" "T1_Library1:1956200" "T1_Library1:1956585" #> [349] "T1_Library1:1956528" "T1_Library1:1955287" "T1_Library1:1957225" #> [352] "T1_Library1:1957226" "T1_Library1:1957227" "T1_Library1:1956586" #> [355] "T1_Library1:1956407" "T1_Library1:1957235" "T1_Library1:1957239" #> [358] "T1_Library1:1957240" "T1_Library1:1956351" "T1_Library1:1956479" #> [361] "T1_Library1:1957244" "T1_Library1:1955733" "T1_Library1:1957248" #> [364] "T1_Library1:1955620" "T1_Library1:1956215" "T1_Library1:1956425" #> [367] "T1_Library1:1955527" "T1_Library1:1956352" "T1_Library1:1957255" #> [370] "T1_Library1:1955528" "T1_Library1:1956422" "T1_Library1:1957256" #> [373] "T1_Library1:1957257" "T1_Library1:1957258" "T1_Library1:1957262" #> #> $`chr14:106327474_C_G`$alt #> [1] "T1_Library1:1956883" "T1_Library1:1957254" #> #> #> $`chr14:106327649_G_T` #> $`chr14:106327649_G_T`$ref #> [1] "T1_Library1:1957616" "T1_Library1:1957623" "T1_Library1:1957624" #> [4] "T1_Library1:1957636" "T1_Library1:1957638" "T1_Library1:1957640" #> [7] "T1_Library1:1957642" "T1_Library1:1957644" "T1_Library1:1957646" #> [10] "T1_Library1:1957651" "T1_Library1:1957653" "T1_Library1:1957657" #> [13] "T1_Library1:1957658" "T1_Library1:1957660" "T1_Library1:1957661" #> [16] "T1_Library1:1957662" "T1_Library1:1957663" "T1_Library1:1957666" #> [19] "T1_Library1:1957667" "T1_Library1:1957673" "T1_Library1:1955987" #> [22] "T1_Library1:1957675" "T1_Library1:1957677" "T1_Library1:1957679" #> [25] "T1_Library1:1957685" "T1_Library1:1957687" "T1_Library1:1957694" #> [28] "T1_Library1:1957699" "T1_Library1:1957700" "T1_Library1:1957701" #> [31] "T1_Library1:1957703" "T1_Library1:1957713" "T1_Library1:1957715" #> [34] "T1_Library1:1957716" "T1_Library1:1957503" "T1_Library1:1957720" #> [37] "T1_Library1:1957722" "T1_Library1:1957283" "T1_Library1:1957324" #> [40] "T1_Library1:1957731" "T1_Library1:1957738" "T1_Library1:1956281" #> [43] "T1_Library1:1956283" "T1_Library1:1956284" "T1_Library1:1956387" #> [46] "T1_Library1:1957153" "T1_Library1:1957200" "T1_Library1:1957244" #> [49] "T1_Library1:1957276" "T1_Library1:1957284" "T1_Library1:1957286" #> [52] "T1_Library1:1957290" "T1_Library1:1957291" "T1_Library1:1957292" #> [55] "T1_Library1:1957325" "T1_Library1:1955344" "T1_Library1:1956989" #> [58] "T1_Library1:1956990" "T1_Library1:1957288" "T1_Library1:1957336" #> [61] "T1_Library1:1957444" "T1_Library1:1957746" "T1_Library1:1957748" #> [64] "T1_Library1:1957749" "T1_Library1:1957750" "T1_Library1:1957752" #> [67] "T1_Library1:1957754" "T1_Library1:1957762" "T1_Library1:1957766" #> [70] "T1_Library1:1957768" "T1_Library1:1957770" "T1_Library1:1957277" #> [73] "T1_Library1:1957778" "T1_Library1:1957779" "T1_Library1:1957780" #> [76] "T1_Library1:1957781" "T1_Library1:1957788" "T1_Library1:1957789" #> [79] "T1_Library1:1957790" "T1_Library1:1957796" "T1_Library1:1957798" #> [82] "T1_Library1:1957799" "T1_Library1:1957800" "T1_Library1:1957805" #> [85] "T1_Library1:1957807" "T1_Library1:1957815" "T1_Library1:1957823" #> [88] "T1_Library1:1957826" "T1_Library1:1957331" "T1_Library1:1957832" #> [91] "T1_Library1:1957836" "T1_Library1:1956235" "T1_Library1:1956341" #> [94] "T1_Library1:1956463" "T1_Library1:1956977" "T1_Library1:1956978" #> [97] "T1_Library1:1957255" "T1_Library1:1957258" "T1_Library1:1957300" #> [100] "T1_Library1:1956992" "T1_Library1:1957846" "T1_Library1:1957848" #> [103] "T1_Library1:1957851" "T1_Library1:1957858" "T1_Library1:1957867" #> [106] "T1_Library1:1957868" "T1_Library1:1957870" "T1_Library1:1957871" #> [109] "T1_Library1:1957872" "T1_Library1:1957873" "T1_Library1:1954685" #> [112] "T1_Library1:1957343" "T1_Library1:1957363" "T1_Library1:1957881" #> [115] "T1_Library1:1957883" "T1_Library1:1957884" "T1_Library1:1957888" #> [118] "T1_Library1:1957889" "T1_Library1:1957890" "T1_Library1:1957892" #> [121] "T1_Library1:1957345" "T1_Library1:1957898" "T1_Library1:1957901" #> [124] "T1_Library1:1957903" "T1_Library1:1957909" "T1_Library1:1957910" #> [127] "T1_Library1:1957914" "T1_Library1:1957915" "T1_Library1:1957916" #> [130] "T1_Library1:1957918" "T1_Library1:1957374" "T1_Library1:1957923" #> [133] "T1_Library1:1957925" "T1_Library1:1957239" "T1_Library1:1957364" #> [136] "T1_Library1:1957365" "T1_Library1:1957927" "T1_Library1:1957933" #> [139] "T1_Library1:1957938" "T1_Library1:1957580" "T1_Library1:1957941" #> [142] "T1_Library1:1957945" "T1_Library1:1957949" "T1_Library1:1957950" #> [145] "T1_Library1:1957955" "T1_Library1:1957957" "T1_Library1:1957970" #> [148] "T1_Library1:1957971" "T1_Library1:1957974" "T1_Library1:1957979" #> [151] "T1_Library1:1957980" "T1_Library1:1957982" "T1_Library1:1957986" #> [154] "T1_Library1:1957987" "T1_Library1:1957990" "T1_Library1:1957993" #> [157] "T1_Library1:1957997" "T1_Library1:1957998" "T1_Library1:1958004" #> [160] "T1_Library1:1958008" "T1_Library1:1958010" "T1_Library1:1958011" #> [163] "T1_Library1:1957498" "T1_Library1:1958012" "T1_Library1:1958013" #> [166] "T1_Library1:1958014" "T1_Library1:1958023" "T1_Library1:1957417" #> [169] "T1_Library1:1958027" "T1_Library1:1958033" "T1_Library1:1958034" #> [172] "T1_Library1:1958036" "T1_Library1:1958037" "T1_Library1:1958044" #> [175] "T1_Library1:1958047" "T1_Library1:1958051" "T1_Library1:1958053" #> [178] "T1_Library1:1958054" "T1_Library1:1958058" "T1_Library1:1958061" #> [181] "T1_Library1:1958066" "T1_Library1:1958069" "T1_Library1:1958070" #> [184] "T1_Library1:1958074" "T1_Library1:1958077" "T1_Library1:1958079" #> [187] "T1_Library1:1958084" "T1_Library1:1958086" "T1_Library1:1956618" #> [190] "T1_Library1:1957421" "T1_Library1:1957422" "T1_Library1:1957473" #> [193] "T1_Library1:1957568" "T1_Library1:1958099" "T1_Library1:1958102" #> [196] "T1_Library1:1958108" "T1_Library1:1958110" "T1_Library1:1957452" #> [199] "T1_Library1:1957463" "T1_Library1:1958114" "T1_Library1:1958117" #> [202] "T1_Library1:1958118" "T1_Library1:1958120" "T1_Library1:1958122" #> [205] "T1_Library1:1956201" "T1_Library1:1956573" "T1_Library1:1957293" #> [208] "T1_Library1:1957367" "T1_Library1:1957396" "T1_Library1:1957404" #> [211] "T1_Library1:1958132" "T1_Library1:1958136" "T1_Library1:1958144" #> [214] "T1_Library1:1958146" "T1_Library1:1958148" "T1_Library1:1958152" #> [217] "T1_Library1:1957564" "T1_Library1:1958163" "T1_Library1:1958164" #> [220] "T1_Library1:1958166" "T1_Library1:1958169" "T1_Library1:1958170" #> [223] "T1_Library1:1958176" "T1_Library1:1958177" "T1_Library1:1958180" #> [226] "T1_Library1:1958182" "T1_Library1:1958186" "T1_Library1:1958188" #> [229] "T1_Library1:1958191" "T1_Library1:1958195" "T1_Library1:1958198" #> [232] "T1_Library1:1958200" "T1_Library1:1958203" "T1_Library1:1957409" #> [235] "T1_Library1:1957540" "T1_Library1:1958206" "T1_Library1:1957381" #> [238] "T1_Library1:1957541" "T1_Library1:1958209" "T1_Library1:1958213" #> [241] "T1_Library1:1958217" "T1_Library1:1958219" "T1_Library1:1958224" #> [244] "T1_Library1:1958225" "T1_Library1:1956508" "T1_Library1:1957393" #> [247] "T1_Library1:1957428" "T1_Library1:1957522" "T1_Library1:1957614" #> [250] "T1_Library1:1958228" "T1_Library1:1957383" "T1_Library1:1957465" #> [253] "T1_Library1:1957486" "T1_Library1:1957507" "T1_Library1:1957586" #> [256] "T1_Library1:1958232" "T1_Library1:1958235" "T1_Library1:1958237" #> [259] "T1_Library1:1957456" "T1_Library1:1957469" "T1_Library1:1957483" #> [262] "T1_Library1:1958238" "T1_Library1:1958241" "T1_Library1:1958243" #> [265] "T1_Library1:1958244" "T1_Library1:1958245" "T1_Library1:1957487" #> [268] "T1_Library1:1958249" "T1_Library1:1958252" "T1_Library1:1958261" #> [271] "T1_Library1:1957572" "T1_Library1:1957201" "T1_Library1:1958264" #> [274] "T1_Library1:1958265" "T1_Library1:1958268" "T1_Library1:1958269" #> [277] "T1_Library1:1958271" "T1_Library1:1958274" "T1_Library1:1958278" #> [280] "T1_Library1:1958284" "T1_Library1:1958285" "T1_Library1:1958288" #> [283] "T1_Library1:1958290" "T1_Library1:1958293" "T1_Library1:1958309" #> [286] "T1_Library1:1958315" "T1_Library1:1958321" "T1_Library1:1958325" #> [289] "T1_Library1:1956285" "T1_Library1:1956323" "T1_Library1:1956324" #> [292] "T1_Library1:1958331" "T1_Library1:1955014" "T1_Library1:1955832" #> [295] "T1_Library1:1956149" "T1_Library1:1957168" "T1_Library1:1957434" #> [298] "T1_Library1:1957435" "T1_Library1:1957471" "T1_Library1:1957526" #> [301] "T1_Library1:1957601" "T1_Library1:1958336" "T1_Library1:1958338" #> [304] "T1_Library1:1955263" "T1_Library1:1958349" "T1_Library1:1958351" #> [307] "T1_Library1:1958353" "T1_Library1:1957046" "T1_Library1:1957278" #> [310] "T1_Library1:1957355" "T1_Library1:1957528" "T1_Library1:1958362" #> [313] "T1_Library1:1958366" "T1_Library1:1958368" "T1_Library1:1958373" #> [316] "T1_Library1:1958376" "T1_Library1:1956666" "T1_Library1:1956731" #> [319] "T1_Library1:1958384" "T1_Library1:1956819" "T1_Library1:1957547" #> [322] "T1_Library1:1958386" "T1_Library1:1958389" "T1_Library1:1958391" #> [325] "T1_Library1:1958393" "T1_Library1:1956639" "T1_Library1:1957549" #> [328] "T1_Library1:1957490" "T1_Library1:1958398" "T1_Library1:1956532" #> [331] "T1_Library1:1958404" "T1_Library1:1956640" "T1_Library1:1956641" #> [334] "T1_Library1:1957457" "T1_Library1:1957605" "T1_Library1:1958407" #> [337] "T1_Library1:1956443" "T1_Library1:1958412" "T1_Library1:1958415" #> [340] "T1_Library1:1958417" "T1_Library1:1958420" "T1_Library1:1956715" #> [343] "T1_Library1:1956716" "T1_Library1:1958423" "T1_Library1:1958424" #> [346] "T1_Library1:1958425" "T1_Library1:1958429" "T1_Library1:1957294" #> [349] "T1_Library1:1957550" "T1_Library1:1958431" "T1_Library1:1958433" #> [352] "T1_Library1:1957606" "T1_Library1:1958440" "T1_Library1:1958443" #> [355] "T1_Library1:1958444" "T1_Library1:1958446" "T1_Library1:1957690" #> [358] "T1_Library1:1958450" "T1_Library1:1958451" "T1_Library1:1954756" #> [361] "T1_Library1:1958453" "T1_Library1:1958454" "T1_Library1:1958455" #> [364] "T1_Library1:1958460" "T1_Library1:1958461" "T1_Library1:1958463" #> [367] "T1_Library1:1958466" "T1_Library1:1958469" "T1_Library1:1956398" #> #> $`chr14:106327649_G_T`$alt #> [1] "T1_Library1:1956883" "T1_Library1:1957254" "T1_Library1:1958449" #> #> #> $`chr14:106327759_A_T` #> $`chr14:106327759_A_T`$ref #> [1] "T1_Library1:1958509" "T1_Library1:1958510" "T1_Library1:1957766" #> [4] "T1_Library1:1958512" "T1_Library1:1958514" "T1_Library1:1958517" #> [7] "T1_Library1:1957140" "T1_Library1:1957141" "T1_Library1:1958166" #> [10] "T1_Library1:1953870" "T1_Library1:1957858" "T1_Library1:1957910" #> [13] "T1_Library1:1958519" "T1_Library1:1958520" "T1_Library1:1958525" #> [16] "T1_Library1:1958527" "T1_Library1:1958528" "T1_Library1:1958531" #> [19] "T1_Library1:1958534" "T1_Library1:1957492" "T1_Library1:1957738" #> [22] "T1_Library1:1957867" "T1_Library1:1958004" "T1_Library1:1958132" #> [25] "T1_Library1:1956945" "T1_Library1:1957923" "T1_Library1:1958051" #> [28] "T1_Library1:1958114" "T1_Library1:1958191" "T1_Library1:1955551" #> [31] "T1_Library1:1956511" "T1_Library1:1956757" "T1_Library1:1956773" #> [34] "T1_Library1:1957800" "T1_Library1:1957889" "T1_Library1:1957970" #> [37] "T1_Library1:1957971" "T1_Library1:1958053" "T1_Library1:1958054" #> [40] "T1_Library1:1958077" "T1_Library1:1958079" "T1_Library1:1958110" #> [43] "T1_Library1:1958117" "T1_Library1:1958136" "T1_Library1:1958152" #> [46] "T1_Library1:1958169" "T1_Library1:1958213" "T1_Library1:1957974" #> [49] "T1_Library1:1958238" "T1_Library1:1958431" "T1_Library1:1958546" #> [52] "T1_Library1:1958547" "T1_Library1:1958548" "T1_Library1:1957481" #> [55] "T1_Library1:1958235" "T1_Library1:1958550" "T1_Library1:1958554" #> [58] "T1_Library1:1958557" "T1_Library1:1958559" "T1_Library1:1957555" #> [61] "T1_Library1:1958561" "T1_Library1:1958563" "T1_Library1:1958566" #> [64] "T1_Library1:1958568" "T1_Library1:1958206" "T1_Library1:1958268" #> [67] "T1_Library1:1958570" "T1_Library1:1958571" "T1_Library1:1958572" #> [70] "T1_Library1:1958573" "T1_Library1:1956099" "T1_Library1:1956574" #> [73] "T1_Library1:1957047" "T1_Library1:1957061" "T1_Library1:1957240" #> [76] "T1_Library1:1957673" "T1_Library1:1957846" "T1_Library1:1957868" #> [79] "T1_Library1:1957914" "T1_Library1:1957979" "T1_Library1:1957980" #> [82] "T1_Library1:1958008" "T1_Library1:1958058" "T1_Library1:1958195" #> [85] "T1_Library1:1958271" "T1_Library1:1958274" "T1_Library1:1958278" #> [88] "T1_Library1:1958325" "T1_Library1:1958575" "T1_Library1:1956900" #> [91] "T1_Library1:1957651" "T1_Library1:1958245" "T1_Library1:1958386" #> [94] "T1_Library1:1958577" "T1_Library1:1958581" "T1_Library1:1958583" #> [97] "T1_Library1:1958585" "T1_Library1:1958591" "T1_Library1:1958284" #> [100] "T1_Library1:1958285" "T1_Library1:1958118" "T1_Library1:1958595" #> [103] "T1_Library1:1958598" "T1_Library1:1957826" "T1_Library1:1958407" #> [106] "T1_Library1:1957982" "T1_Library1:1958182" "T1_Library1:1956390" #> [109] "T1_Library1:1958120" "T1_Library1:1958170" "T1_Library1:1958602" #> [112] "T1_Library1:1958604" "T1_Library1:1958198" "T1_Library1:1958605" #> [115] "T1_Library1:1958607" "T1_Library1:1958609" "T1_Library1:1958010" #> [118] "T1_Library1:1958433" "T1_Library1:1958613" "T1_Library1:1958615" #> [121] "T1_Library1:1956822" "T1_Library1:1957607" "T1_Library1:1958228" #> [124] "T1_Library1:1958288" "T1_Library1:1958290" "T1_Library1:1958498" #> [127] "T1_Library1:1958617" "T1_Library1:1958264" "T1_Library1:1958618" #> [130] "T1_Library1:1956078" "T1_Library1:1956079" "T1_Library1:1958293" #> [133] "T1_Library1:1958349" "T1_Library1:1958362" "T1_Library1:1958619" #> [136] "T1_Library1:1958620" "T1_Library1:1958621" "T1_Library1:1958624" #> [139] "T1_Library1:1958144" "T1_Library1:1958629" "T1_Library1:1958631" #> [142] "T1_Library1:1958633" "T1_Library1:1958634" "T1_Library1:1958637" #> [145] "T1_Library1:1958638" "T1_Library1:1958639" "T1_Library1:1958224" #> [148] "T1_Library1:1958331" "T1_Library1:1958640" "T1_Library1:1958642" #> [151] "T1_Library1:1958217" "T1_Library1:1958389" "T1_Library1:1957145" #> [154] "T1_Library1:1958338" "T1_Library1:1958440" "T1_Library1:1958645" #> [157] "T1_Library1:1958650" "T1_Library1:1957182" "T1_Library1:1957303" #> [160] "T1_Library1:1957332" "T1_Library1:1957986" "T1_Library1:1958653" #> [163] "T1_Library1:1958655" "T1_Library1:1958656" "T1_Library1:1958660" #> [166] "T1_Library1:1958662" "T1_Library1:1958666" "T1_Library1:1958667" #> [169] "T1_Library1:1958366" "T1_Library1:1958672" "T1_Library1:1957092" #> [172] "T1_Library1:1958391" "T1_Library1:1958684" "T1_Library1:1958689" #> [175] "T1_Library1:1958693" "T1_Library1:1958694" "T1_Library1:1958701" #> [178] "T1_Library1:1958704" "T1_Library1:1958708" "T1_Library1:1958712" #> [181] "T1_Library1:1957873" "T1_Library1:1958714" "T1_Library1:1958720" #> [184] "T1_Library1:1956823" "T1_Library1:1958011" "T1_Library1:1958351" #> [187] "T1_Library1:1958384" "T1_Library1:1957016" "T1_Library1:1957333" #> [190] "T1_Library1:1957653" "T1_Library1:1958061" "T1_Library1:1958265" #> [193] "T1_Library1:1958443" "T1_Library1:1958723" "T1_Library1:1958423" #> [196] "T1_Library1:1956329" "T1_Library1:1957048" "T1_Library1:1958309" #> [199] "T1_Library1:1958444" "T1_Library1:1958453" "T1_Library1:1958454" #> [202] "T1_Library1:1958471" "T1_Library1:1957147" "T1_Library1:1958368" #> [205] "T1_Library1:1958424" "T1_Library1:1958353" "T1_Library1:1958728" #> [208] "T1_Library1:1958412" "T1_Library1:1958460" "T1_Library1:1958472" #> [211] "T1_Library1:1958393" "T1_Library1:1958461" "T1_Library1:1958731" #> [214] "T1_Library1:1958733" "T1_Library1:1958738" "T1_Library1:1958739" #> [217] "T1_Library1:1958404" "T1_Library1:1958744" "T1_Library1:1958269" #> [220] "T1_Library1:1958759" "T1_Library1:1958761" "T1_Library1:1958146" #> [223] "T1_Library1:1958483" "T1_Library1:1958766" "T1_Library1:1958772" #> [226] "T1_Library1:1958774" "T1_Library1:1958200" "T1_Library1:1952749" #> [229] "T1_Library1:1957441" "T1_Library1:1957987" "T1_Library1:1958315" #> [232] "T1_Library1:1958425" "T1_Library1:1958775" "T1_Library1:1958783" #> [235] "T1_Library1:1958786" "T1_Library1:1958420" "T1_Library1:1958790" #> [238] "T1_Library1:1958795" "T1_Library1:1957257" "T1_Library1:1958798" #> [241] "T1_Library1:1958801" "T1_Library1:1958805" "T1_Library1:1958806" #> [244] "T1_Library1:1958808" "T1_Library1:1958812" "T1_Library1:1958819" #> [247] "T1_Library1:1958823" "T1_Library1:1958474" "T1_Library1:1958830" #> [250] "T1_Library1:1958832" "T1_Library1:1958836" "T1_Library1:1958843" #> [253] "T1_Library1:1958846" "T1_Library1:1958848" "T1_Library1:1958851" #> [256] "T1_Library1:1958857" "T1_Library1:1958865" "T1_Library1:1958867" #> [259] "T1_Library1:1958871" "T1_Library1:1958881" "T1_Library1:1958889" #> [262] "T1_Library1:1958891" "T1_Library1:1958897" "T1_Library1:1958899" #> [265] "T1_Library1:1958900" "T1_Library1:1958902" "T1_Library1:1958446" #> [268] "T1_Library1:1958455" "T1_Library1:1958463" "T1_Library1:1958486" #> [271] "T1_Library1:1958905" "T1_Library1:1958907" "T1_Library1:1958488" #> [274] "T1_Library1:1958909" "T1_Library1:1958911" "T1_Library1:1958912" #> [277] "T1_Library1:1958466" "T1_Library1:1958919" "T1_Library1:1958922" #> [280] "T1_Library1:1958925" "T1_Library1:1958927" "T1_Library1:1958930" #> [283] "T1_Library1:1958932" "T1_Library1:1958934" "T1_Library1:1958937" #> [286] "T1_Library1:1958941" "T1_Library1:1953178" "T1_Library1:1958186" #> [289] "T1_Library1:1958225" "T1_Library1:1958502" "T1_Library1:1958945" #> [292] "T1_Library1:1956755" "T1_Library1:1958946" "T1_Library1:1958949" #> [295] "T1_Library1:1958950" "T1_Library1:1958952" "T1_Library1:1958961" #> [298] "T1_Library1:1958962" "T1_Library1:1957326" "T1_Library1:1958969" #> [301] "T1_Library1:1957148" "T1_Library1:1958219" "T1_Library1:1958981" #> [304] "T1_Library1:1958984" "T1_Library1:1958997" "T1_Library1:1957517" #> [307] "T1_Library1:1958450" "T1_Library1:1958451" "T1_Library1:1959000" #> [310] "T1_Library1:1959002" "T1_Library1:1959003" "T1_Library1:1959004" #> [313] "T1_Library1:1959005" "T1_Library1:1959009" "T1_Library1:1959011" #> [316] "T1_Library1:1959012" "T1_Library1:1959015" "T1_Library1:1959022" #> [319] "T1_Library1:1959026" "T1_Library1:1958478" "T1_Library1:1959032" #> [322] "T1_Library1:1959033" "T1_Library1:1959034" "T1_Library1:1959040" #> [325] "T1_Library1:1959041" "T1_Library1:1959044" "T1_Library1:1959045" #> [328] "T1_Library1:1959049" "T1_Library1:1959050" "T1_Library1:1959051" #> [331] "T1_Library1:1958490" "T1_Library1:1959058" "T1_Library1:1959062" #> [334] "T1_Library1:1957442" #> #> $`chr14:106327759_A_T`$alt #> [1] "T1_Library1:1958782" #> #>