get consensus sequence from bam file with insertions
Hello everyone! I want to get consensus sequence from my NGS data. I created sorted bam, and visualized it in IGV. I know that alligment has SNPs, insertions and deletions. After that I tried to get consensus sequence from my NGS data. I used two ways:
- From samtools manual: "Generate the consensus sequence for one diploid individual:
samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fq" - this coomand gave me only SNPs in consensus sequence. - Copy consensus sequence from IGV. It gave me consensus with SNPs and deletions.
How can I get insertions in consensus sequence?
Thanks!
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Please use the formatting bar (especially the
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Have you tried this?
Yes, but in this try result sequence has same length as a reference. But region with reads is much less.
Could you please show a screenshot of a region where you suppose an indel?
More information. I used command:
But insertions and deletions were not find in consensus.
This is part with deletion: https://ibb.co/27jVv4S
I saw this post: https://www.biostars.org/p/179357/ With sam=1.3, but than I tried
with bam file from bbmap it was not work. The report was: The sequence "chr3B chr3B:12400161..12411680" not found (this is my reference name). Maybe problems with indels can be associated with cigar sting? Different formats or something like that?
Did you resolve this problem?
Please be specific about what problem.