How to deal with the sam file without the
header:
You can produce this with the faidx command in
samtools:
samtools faidx
all_sequences.fa
then use the output
samtools view
-bS -t all_sequences.fai infile.sam > outfile.bam
where all_sequence.fa is the whole genome fasta file, and infile.sam is the samfile without the header.
No comments:
Post a Comment