VarScan fpfilter returning no results

[ernfrid]

Moving this from comment on other issue

Hi,

I am using bam-readcount (0.7.4) , as part of varscan somatic pipeline, but while applying fpfilter, getting error saying "failed because no readcounts were returned"... What could be the reason I am not able to figure out, what could be the reason for this...

LOG: 740 variants in input file 0 had a bam-readcount result 0 had reads1>=2 0 passed filters 740 failed filters 740 failed because no readcounts were returned 0 failed minimim variant count < 3 0 failed minimum variant freq < 0.05 0 failed minimum strandedness < 0.0 0 failed minimum reference readpos < 0.2 0 failed minimum variant readpos < 0.15 0 failed minimum reference dist3 < 0.2 0 failed minimum variant dist3 < 0.15 0 failed maximum reference MMQS > 50 0 failed maximum variant MMQS > 100 0 failed maximum MMQS diff (var - ref) > 50 0 failed maximum mapqual diff (ref - var) > 10 0 failed minimim ref mapqual < 20 0 failed minimim var mapqual < 30 0 failed minimim ref basequal < 15 0 failed minimim var basequal < 30 0 failed maximum RL diff (ref - var) > 0.05

Thanks, Vt,

[ernfrid]

I've run into similar problems before and in that case the issue was that my fasta file was not indexed with samtools faidx. Is your reference sequence indexed?

[jgarces02]

Hi, I've a similar problem. In my case, I've created an index with samtools but it doesn't work either... That curious because the stdout has the following message and generates a (empty) file called .readcounts:

Minimum mapping quality is set to 1
Expect library: SureSelect in BAM

This is the command I'm using:

 ./bam-readcount -b 15 -q 1 -f path/to/reference/fasta -l path/to/VarScan.indel path/to/tumorBam