What is the best way to detect large indels ? I mapped reads of whole genome shotgun sequencing against the reference sequences.
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written
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nakanomasayuki265 •
2 answers
The best way to detect large deletions is to map with BBMap and call variants with the BBMap package's CallVariants tool. BBMap can also detect moderate-sized insertions (up to 60% of insert size, or so). For example:
bbmap.sh in=reads.fq out=mapped.sam ref=ref.fa maxindel=400k
callvariants.sh in=mapped.sam out=vars.vcf ref=ref.fa ploidy=2
For longer insertions that cannot be captured within a read pair it's probably better to use an indel-specific caller based on coverage and read pairing. But for insertions shorter than ~60% of insert size it's better to merge reads, map them, and call them with a normal variant-caller. I've used BBMerge -> BBMap -> CallVariants successfully with >200bp insertions from 2x100bp reads.
Note that I wrote BBMap and I am biased.
Some good tools are:
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