Entering edit mode
10.1 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
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?
Thanks for your reply and sorry for my late response. I no longer use bam-readcounts.