bam-readcounts: failed to get readcounts for variant allele
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Entering edit mode
7.3 years ago
anat • 0

Hello

I am trying to run bam-readcounts and fpfilter.pl on my VarScan2 output but most of my variants "failed to get readcounts for variant allele".

My output is not vcf and I did not find anything related to lower and upper cases (as was mentioned in another forum).

Any idea what might be the problem?

Thanks!

Anat

bam-readcounts command line:

bam-readcount \
  -q 1 \
  -b 20 \
  -f /media/Data/Anat_Data/Ref_genome/human_g1k_v37.fasta \
  no_R2_mapped_sorted.bam \
  -l /media/localData/Anat/HCC_mut/DesignDocument/full_Regions_new output.basename.copy.snp.Somatic \
  > varScan.variants.copy.snp.Somatic.readcounts

fpfilter command line:

perl /usr/local/bin/fpfilter.pl \
  output.basename.copy.snp.Somatic.hc.filter \
  varScan.variants.copy.snp.Somatic.readcounts \
  --output-basename varScan.copy.snp.Somatic.hc.filter

output:

18 variants
17 failed to get readcounts for variant allele
0 had read position < 0.1
0 had strandedness < 0.01
1 had var_count < 4
0 had var_freq < 0.05
0 had mismatch qualsum difference > 50
0 had mapping quality difference > 30
0 had read length difference > 25
0 had var_distance_to_3' < 0.2
0 passed the strand filter
bam-readcounts VarScan2 • 2.4k views
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Entering edit mode

Can you indicate what software versions you are using? Also, based on your filenames it looks like you are only examining single nucleotide variants (not indels), is that correct?

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Entering edit mode

Thanks for your reply and sorry for my late response. I no longer use bam-readcounts.

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