Error in SAMTools mpileup
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5.8 years ago
julia92796 • 0

I have a BAM file containing an alignment of the neanderthal y chromosome to the human y chromosome. I'm trying to extract the consensus sequence of the neanderthal reads so that I can isolate genes. I found this command online:

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

and am trying to use it to output the consensus sequence. However, I keep getting an error:

Error: Could not parse --min-ac g Use of uninitialized value $l in numeric lt (<) at vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at vcfutils.pl line 566.
<mpileup> Set max per-file depth to 8000

Does anyone know how to fix this? If not, is there an alternate method to get a consensus sequence from reads?

SAMTools mpileup consensus sequence software error • 1.8k views
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I also encounter the similar problem, and haven't resolved this yet.

Is there anyone who knows what's wrong with this error?

Thanks a lot. : )

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