get consensus sequence from bam file with insertions

Question

[Vvedenskiia]

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:

1. 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.
2. Copy consensus sequence from IGV. It gave me consensus with SNPs and deletions.

How can I get insertions in consensus sequence?

Thanks!

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), 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.

[finswimmer]

Have you tried this?

• Generating consensus sequence from bam file

[Vvedenskiia]

Yes, but in this try result sequence has same length as a reference. But region with reads is much less.

[finswimmer]

Could you please show a screenshot of a region where you suppose an indel?

[Vvedenskiia]

More information. I used command:

bcftools consensus -f ref.fasta -s sorted_03.bam vars3_1.vcf.gz >out.fa

But insertions and deletions were not find in consensus.

[Vvedenskiia]

This is part with deletion: https://ibb.co/27jVv4S

[Vvedenskiia]

I saw this post: https://www.biostars.org/p/179357/ With sam=1.3, but than I tried

samtools mpileup -uf SA05sequence.fasta sorted.bam | bcftools call -c > vars.vcf

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?

[yichen503]

Did you resolve this problem?

[GenoMax]

Please be specific about what problem.