Question: bam-readcounts: failed to get readcounts for variant allele
0
gravatar for anat
3.6 years ago by
anat0
Israel
anat0 wrote:

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 comman 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

varscan2 bam-readcounts • 1.4k views
ADD COMMENTlink modified 3.5 years ago • written 3.6 years ago by anat0

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?

ADD REPLYlink written 3.6 years ago by ernfrid190
0
gravatar for anat
3.5 years ago by
anat0
Israel
anat0 wrote:

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

ADD COMMENTlink written 3.5 years ago by anat0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1271 users visited in the last hour