bam-readcount error Expect Library

Question

[9521ljh]

After i do

java -jar varscan.jar processSomatic output.basename.snp

Then, i get output.base.snp.Somatic.hc.filter

Then to execute False Positive Filter:

bam-readcount -q 1 -b 20 -f reference.fasta -l output.base.snp.Somatic.hc.filter tumorfile.bam >varscan.variants.readcounts

but the output give me

Expect Library: LB in BAM

what is wrong? , i can't understand what should i input after " -l "

Answer 1

[Pierre Lindenbaum]

as far as I understand, there is no read group with a LB attribute. https://software.broadinstitute.org/gatk/documentation/article?id=6472

Answer 2

[ATpoint]

Probably the input file for -l is malformatted. It must be a BED file with chr-start-end. The documentation, depending on which website you check (original VarScan page, GitHub, the VarScan2 how-to paper) is misleading at times. Given a VCF file, just do:

awk '$1 ~ /^#/ {next} {print $1, $2-1, $2}' in.vcf | sort -k1,1 -k2,2n -u > out.bed