Vanessa Souza

Hi, Dan, I'm new to bioinformatics. Could you explain in detail how to prepare BED-like var file for bamreadcount. As suggested for SNV that I use print $1,$2,$2, but for indels I didn’t understand exactly how to proceed. I believe this is the cause of my problem.

perl script_FPfilter sample.varScan.snp.filter.bed varScan.variants.readcounts –output-basename varScan.variants.filter I get the following output: 27841 variants 27841 failed to get readcounts for variant allele 0 had read position < 0.1 0 had strandedness < 0.01 0 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 Apparently, the problem is...

I did it, but my problem remains.

I did it, but my problem remains.

I did it, but my problem remains.

Do you able to solve the problem of failure in the result because no read count was returned? I'm having the same problem.

I'm new to variant calling and I'm having trouble running VarScan2 v2.4.4 (Support Protocol 1) which can be found in the following online document: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278659 / The authors advise using the fpfilter.pl accessory script (https://sourceforge.net/projects/varscan/files/scripts/). When I run the following command: perl script_FPfilter sample.varScan.snp.filter.bed varScan.variants.readcounts –output-basename varScan.variants.filter I get the following output:...