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bede/sam_to_consensus_fa.sh

Last active July 17, 2017 17:15
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Bioinformatics code golf: SAM to consensus FASTA
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sam_to_consensus_fa.sh
# SAM to consensus FASTA code golf, inspired by http://lab.loman.net/2015/07/28/calling-haploid-consensus-sequence/
# Starting with a SAM:
samtools view -bS seqs.sam | samtools sort - seqs # Generate and sort BAM
samtools index seqs.bam # Index BAM
# Starting with an indexed BAM:
samtools mpileup -ud 1000 -f seqs_ref.fasta seqs.bam | bcftools call -c | vcfutils.pl vcf2fq | seqtk seq -a - > seqs.consensus.fa # Generate pileup, call variants, convert to fq, convert to fa
# Who can do better? The bar is set low...
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bede commented Sep 16, 2015

@nickloman suggests FreeBayes
http://lab.loman.net/2015/07/28/calling-haploid-consensus-sequence/

freebayes -f ref.fa -p 1 aln.sorted.bam > vcffile
vcf2fasta -f ref.fa -P 1 vcffile

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