Hello,
I want to replace the CIGAR strings of SAM/BAM file without changing anything else so that the soft-clipped bases are shown as matches/mismatches.
e.g. 11S60M becomes 71M
15M1D40M15S becomes 15M1D55M
How can I do this?
I have a genome with N's between the contigs. I want to fill these regions using overhangs. The length of N's may be incorrect. I aligned my reads with BWA-mem, and will get the consensus seq using samtools mpileup. I thought this would be the best approach.
Thank you
I want to replace the CIGAR strings of SAM/BAM file without changing anything else so that the soft-clipped bases are shown as matches/mismatches.
e.g. 11S60M becomes 71M
15M1D40M15S becomes 15M1D55M
How can I do this?
I have a genome with N's between the contigs. I want to fill these regions using overhangs. The length of N's may be incorrect. I aligned my reads with BWA-mem, and will get the consensus seq using samtools mpileup. I thought this would be the best approach.
Thank you
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