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bam-readcount empty output

Hi,

I am using bam-readcount. However, when I run the following input I get a blank output;

$ bam-readcount -f NCBI_ReferenceGenome.fna -l decomposed.vcf Bowtie2.bam [-b 20] > output.readcount

After running the script, I get the following;

Minimum mapping quality is set to 0
Expect library: Bowtie2 in BAM

The documentation says the output should be a tab-delimited file with column names, however output.readcount is empty. Assuming maybe my files are the problem, I should still get the column names in the output, right? I am a novice and am not sure where to look further in troubleshooting.

Thank you for your help

Protocol

bam-readcount Documentation

sam bam-readcount bam
• 1,342 views • link
written by D_Jens • D_Jens

1 answer

The file given to -l should be a tab-sep file (chr-start-end) not a VCF.

• 0 views • link
written by ATpoint ATpoint

I went back and converted my BAM files to BED files and it worked! Thank you!

• 0 views • link
written by D_Jens • D_Jens

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