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# 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...