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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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something wrong with the total depth output of mpileup #965

Closed liufengxia99 closed 7 years ago

liufengxia99 commented 7 years ago

Subject of the issue

the depth not right, much less than the

Your environment

samtools 1.3.1 or 1.5

Steps to reproduce

/gpfs/software/pipeline/pipeline/tools/samtools mpileup -d 100000 -f /gpfs/software/pipeline/pipeline/database/ref/hg19/hg19.fasta -l /gpfs/software/pipeline/pipeline/region/region_59_188k/region_59_188_merged.bed /gpfs/project/59gene_188K/project_2samples_20170725.business/baidecheng_cf/qc/mapping/tumor/PM2017072404.final.bam > /gpfs/project/59gene_188K/project_2samples_20170725.business/baidecheng_cf/snv/pair/varscan/PM2017072404.pileup

Expected behaviour

positonal depth is much less than the reality samtools depth -r chr1:11856378-11856378 chr1_11856378.bam
chr1 11856378 2883

Actual behaviour

the depth in my bam should about 2800X, while mpileup output is only 1330X, and the reads between forward and reverse strand diff greatly les tumor.chr1.PM2017072404.pileup.gz|grep -P "chr1\t11856378" chr1 11856378 G 1330 .$.$,$......AAA.A...A.,a,,,AA.Aa,,aaa..A,AAAA.aa,,a.A,aaaa,,,,aaaa,,,,a,,.AAAAAa,,,a,.....AAaaaa,,aaa,a,,a,aaaAA.A.a..AAA.......A..AA,,aaa,,,,a,,,,,,aaaa,A.Aa,,....,.A.,,,..aa,.,a..,A,,A..Aa,,a,AA.A......aa....A.....AA.A.A..A..AAA.a,,a,aaA..AAA.a.AA.A.AA,,aAa,a,,AA..A....A..,....A..A....AAAAA.A...AA..A..A..AAAA,AAA..A...A...A.A..AAAA.A..AAA...AA...A,.AAAA...AA...AA..A..AAAA.A..AAA..AA,aA.AaAa,.....A.AAA.A......A.A..AAA..A...AAAA..A...AA.......AA......aa...A.,A...A..A.AA..AAA.A..A.A..A.AA..A....AA.AAA....AA.AA.,..A..A..A.......AAA...AA..A...A.AAAA...A..A..AA.A..AA.AAAAAAA..A....AA.A.AA...AA.A.A...A....A..A...AA...AA...A.AA.AA.....AA.A..AAAAA.A...AAAA............A..AAA..A.AA.AA.....AAA...AAA...A.AAAAA......A...A..A......A.AA.AAA.AA...AA..A....A...AA.AAA...AA...AA...A..AAA.AAA........aAAA..AA...AA....,aa,,AA..A.AA......AA.AA..AAAA..AA.Aa,,,,A.A..AA.A......AAAA.AAAAA.AA..A..A..A.AA.....AA.A....A.AA.....AA..AAA.AA.AA...A.A.......AA.AAA.AA....A...AA..AA.AA......AA.AA...AA.AAA..A...AA..........A...AA..AA.A...AA...a...A.A.....A.AA....A...A..A..AAAA....A.AAA.AAAAA...AAAAAA....A.....A.A.A,a,,aaAA...A..AA.AA..AAA...A......A...A....AA...AA....A.AAAA.A...A.A....A.AA.A...AA.A.A.AA.A.AA.A.A.aAAA.AAAA..AA.AA.....AA.A.A.......AAA.A..A..A..Aa..A.AA....A.A...A.A..AA.A.AA....AA..AA,AAA.AAAA..AAAA...A.AAAA..A.AAA..AA.A.A.A,AAA....^].^]. [QB]Y^_SSSY`U]]S]B0BBBT[_[?@@???bUTCbbbTeC3DDChgF5CDCAGFFCDDCGGG.CFFigf[ggDG4GDGjjjOlfgCDCDGGCDDFCFFDGDDCSSjgi@ljgddkfkljjjSjldgGFCCCGFGGDFFFGGFCCCDGgleDGFjjUjGlhjFAFjmDCGmGCgjFfGFekjSCGGDGgTmSkmllfmD=miiihkmimfheijegmfiQSgShCGG?GCDkhhhhkdhedjSUeSGFCSCFDGGdhmiTjillfmmBllkldKlSmlll;gggSlclilcemhhjlhmeddShGcggldTmKjcliigjgmfcagglflkeghmjjgTmmmgFjdgSgllkcglUlhcmjgmhTddemgjmhdSmmggFDSjTDggmmjlmmemhhcmdmlmhhmhmdlmfghmmfmmmddhhimhmmmhhmlglmhm@dlmmmmgCDmmmhmFhmlghlmfUhhkfTPhmfilhbgmhfmhhhmSimmmhhlegcmmmmdhhhhlGmmhmmhimhmmmmhmmTefmmmhammdmmmfmghfTmmmhmmdmmffhhmmhdmcgddffSmmTmmmmfSmhhhTmllgflSlgmm]clmlihmmfmmlSeimmdhimmhmhhmfhmiiQmdTVfmmgThddmhlmifchfmlglimmlllllglmggcildlffmcfmmmmmhhelmmhhhmcmhmhhfhhmmhmmmglmmhmmhmimmhmfmhhgfff`ghlelfflQflmQ:fllleemghcmmlcfmm]hfllmhfmhdhmfhhmlhhlmihhgfTlmghGllgemlfmfhgmlhfmlbmhhlmmlmjThmcTmmheccmlheldgmlmmhmhimfCmemmimmlhhhTmhhefhlhfllfimhmlhlhhjlmePgfmhmmmmhmhhmilmmcfmmfhglhghfgcllhifmlmmliahdmhheihgmfmmhmmehRjmhhmhejmllilghjhhmhmhhVhEflmgmmjfdlkkOhmmmmihmmiThjmggGcilhaclmhhmmmhmSiGmmmaBehmh^jelllZmlhLm^dRhmmmhUiggZmghdf^imhggegggjmGifllGmjgig_gmgmmhPgh\lmgjMhEmTgjmThhmmGhGmlhl\dimmfi^medhlmlghlKjldlfEhhmEmm\f_hghGGdldZlh_mlZflgGhGEgg_ggaE]TdhEEDmZEgLiFfhhTdGdheFfelEmIG\FFcGGECD\GGgEGlLlGBhFFDFIEGlG_MGgelBZjhG\CgmdFhgGGdG4fFGDDhcJEFDCCbGGEDOBF_FDFVeV9icCFELTjleDiENECKg<T:FfbfB[ i don't how to supply my bam file

lbergelson commented 7 years ago

Hi @liufengxia99

I think you meant to post this issue to https://github.com/samtools/samtools. Samtools is a set of tools built on the c library htslib. This is htsjdk, a separate library that implements similar functionality in java. It's easy to get us mixed up because we're all under the samtools organization. The development teams are different though without a lot of cross over.

I'm closing this issue since we can't help you with it. Please reopen it in the samtools/samtools repo.