bcftools consensus -m file.bed error
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9 days ago

Hi everyone, with bcftools consensus I'm trying to substitute the regions with low coverage with 'N'.

I made a BED file from the bam file with bedtools:

bedtools genomecov -bga -ibam [file.bam] | awk '$4<5' > low_coverage.bed

output:

1 0 10001 0

1 10001 10002 2

1 10002 10003 4

1 10618 10620 5

1 10620 10621 4

1 10621 10622 1

1 10622 10643 0

And then I tried to use the command:

bcftools consensus -I -m low_coverage.bed [file.vcf.gz] > consensus.fa

but it prints the following error:

"Could not parse tab line, expected 1-based coordinate: 1 0 10001 0 Failed to initialize mask regions"

what can be the problem?

samtools help bcftools bedfile consensus • 54 views
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