[bam-readcount v.0.8.0] Fail to open BAM file –q

Question

[vanessagpds]

I'm running the False Positive Filter recommended in Support Protocol 1 by Koboldt et al (2013) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278659/). The recommendations are:

Obtain metrics for the list of variants:

bam-readcount –q 1 –b 20 –f reference.fasta –l varScan.variants BAM_FILE> varScan.variants.readcounts

When trying to perform the command line:

bam-readcount –q 1 –b 20 –f hg38_genome.fa –l sample.varScan.snp.filter bqsr_output.bam > varScan.variants.readcounts

I get the following output:

Minimum mapping quality is set to 0
open: No such file or directory
Fail to open BAM file –q

I consulted some guidelines and it was suggested that the varScan.variants file should be in bed format. I made the following attempts:

vcf2bed <sample.varScan.snp.filter> varScan.variants.bed

awk '$ 1 ~ / ^ # / {next} {print $ 1, $ 2-1, $ 2}' sample.varScan.snp.filter | sort -k1,1 -k2,2n -u> filter_out.bed

But in both attempts the exit was:

Minimum mapping quality is set to 0
open: No such file or directory
Fail to open BAM file –q

As recommended in the article it is suggested that "A list of variants (SNVs or indels) in VarScan format (tab-delimited; the first five columns must be chromosome, position, reference allele, variant allele)".

So, I also tried:

awk -F '\ t' '{print $ 1, $ 2, $ 4, $ 5, $ 3, $ 6, $ 7, $ 8, $ 9, $ 10}' sample.varScan.snp.filter> snp_filter_out.bed

And the failure remained.

What's wrong?

[bam-readcount version: 0.8.0]

[ATpoint]

Is this scripted or is the command entered by hand? Obviously the -q parameter is not properly parsed (as mapping qual is set to 0, the default rather than 1) and the flag is interpreted as the last parameter of the line (so where the bam s expected). Please clarify how you run this.

[GenoMax]

If you are using a Mac, make sure you have turned off smart quotes and smart hyphens in your keyboard preference. Smart hyphens may look like normal - but are not interpreted by linux appropriately.