bam-readcounts: failed to get readcounts for variant allele

Question

[anat]

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

[ernfrid]

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?

[anat]

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