What are "must have" data types one should extract from WGS .fq data?

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2.5 years ago

optimistsso4co3 ▴ 110

I have multiple .fq whole genomes prepared for variant calling. However, it is quite expensive to repeat the whole pipeline so i wonder what data types are must have to extract?

Right now i am planning to extract the following:

Variants (indels, SNPs), with HaplotypeCaller
Structural variants (<1000 bp long), with Manta

What are some other "must have" i could extract?

wgs • 1.2k views

ADD COMMENT • link updated 2.5 years ago by Pierre Lindenbaum 161k • written 2.5 years ago by optimistsso4co3 ▴ 110

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why just <1000 bp long ?

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 161k

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It's the maximum length generated by Manta for my dataset (~100 bp reads).

ADD REPLY • link 2.5 years ago by optimistsso4co3 ▴ 110

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Do you have a reference for that?

ADD REPLY • link 2.5 years ago by WouterDeCoster 47k

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Nope, i manually measured the length of structural variants after conversion to PLINK format. Now when i think about it i see there might be a crack in my logic due to PLINK limits on allele naming length.

ADD REPLY • link 2.5 years ago by optimistsso4co3 ▴ 110

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bcftools query -f '%INFO/SVLEN\n'  in.vcf | tr -d '-' | sort -n | tail

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 161k

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