have mapped illumina PE reads to the reference genome using BWA and now, would like to get a consensus sequence of the mapped reads- can samtools be used on the aligned bam file??
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See this thread: http://seqanswers.com/forums/showthread.php?t=14565 (and the other thread mentioned in #4 there). -
samtools mpileup -uf /<reference.fasta> <aligned.bam> | bcftools view -bcg - > <intermediate.bcf>
gave me an error: -bash: syntax error near unexpected token "<
I was wondering BCFtools are part of samtools, right?- is this the correct comand?Comment
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You don't literally use < > around the file names.Comment
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has anyone tried this command to generate a consensus file
samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq
but where should I put the output file name???Comment
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Originally posted by mmmm View PostCode:$ samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq > output_file_name
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yes- thanks.
I will ignore the abnormal shapes that appeared after the sequence
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