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?
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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. : )