Comments (2)
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
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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
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Related Issues (20)
- Missing filters in VarScan fpfilter output VCF header HOT 1
- Varscan mpileup2cns error: `Input file(s) were not ready for parsing after 100 5-second cycles`.
- 0 had sufficient coverage for comparison HOT 1
- filtering error - "Too many parsing exceptions encountered" HOT 1
- 2.4.4 "release" is actually source HOT 1
- Strand filter applied when outputting to tabular format but not VCF
- Malformed VCF output
- NumberFormatException in varscan somatic HOT 1
- mpileup2snp do not detect all snps
- Not filtering reverse strand's strand bias
- how to pipe the denovo trio calling?
- How to pipe deovo trio with samtool mpileup? HOT 1
- error download jar, corrupt or incomplete HOT 1
- Reads supporting a variant
- log4j
- two mutations on one pos can't call out
- filter for pielup2cns not working
- Why genotype and depth representations are inconsistent
- varscan2 output can't be fed to snpEff. ID column missing?
- how to filter using vcf from multiple samples generated by mpileup2somatic
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