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dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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the num of +-strand diff greatly（Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev） #23

Closed liufengxia99 closed 7 years ago

liufengxia99 commented 7 years ago

i use the somatic command to call mutations, the num of forward and reverse strands diff greatly, the forward is usually much more than the reverse , and the total depth is also much less than other tools(eg. vardict), nearly half of the vardict's total depth(eg. 1560-804,1272-581)

ref/fwd ref/rev var/fwd var/rev">

664 84 510 71 125 22 194 19 232 2 90 1 231 18 91 3 207 21 67 8 153 24 49 7 152 24 49 7 139 18 47 3 307 14 266 16 1068 89 1005 69 892 136 945 127 1 0 1578 292 1129 69 1096 57 796 22 702 19 2 0 1568 152 596 28 574 29 89 2 117 5 752 79 734 88 696 79 730 54 1128 80 1022 72 1183 70 1041 67 1049 63 923 56 559 106 445 86 113 54 129 48 170 3 121 1 512 49 14 0 229 2 197 2 760 67 683 74

thanks a lot for your help

liufengxia99 commented 7 years ago

the script is as follow: /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 & /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/normal/PM2017072405.final.bam > /gpfs/project/59gene_188K/project_2samples_20170725.business/baidecheng_cf/snv/pair/varscan/PM2017072405.pileup & wait /gpfs/software/pipeline/pipeline/tools/java -Xmx4096m -jar /gpfs/software/pipeline/pipeline/tools/VarScan.v2.4.2.jar somatic /gpfs/project/59gene_188K/project_2samples_20170725.business/baidecheng_cf/snv/pair/varscan/PM2017072405.pileup /gpfs/project/59gene_188K/project_2samples_20170725.business/baidecheng_cf/snv/pair/varscan/PM2017072404.pileup /gpfs/project/59gene_188K/project_2samples_20170725.business/baidecheng_cf/snv/pair/varscan/PM2017072404.paired_varscan --min-coverage 8 --min-coverage-normal 8 --min-coverage-tumor 6 --min-var-freq 0.001 --min-freq-for-hom 0.75 --normal-purity 1.00 --tumor-purity 1.00 --p-value 0.99 --somatic-p-value 0.05 --strand-filter 1 --output-vcf 1

liufengxia99 commented 7 years ago

fixed! there is somthing wrong with samtools version 1.3.1 and 1.5 command mpileup ,the total depth is much less than the reality, and also the reverse strands reads count less than reality

samtool version 0.1.19 works