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Is it possible to use CRISP to working with low coverage WGS data? #31

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raksasa opened this issue Sep 8, 2022 · 1 comment
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Is it possible to use CRISP to working with low coverage WGS data? #31

raksasa opened this issue Sep 8, 2022 · 1 comment

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@raksasa
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raksasa commented Sep 8, 2022

Hi,
I'm trying to call indel from many low coverage WGS data from many individuals. I guess I can improve indel calling sensitivity if I treat them as pool-seq. Is it fine to use CRISP to work with such data? If yes, how should I specify parameter '--bam'? I guessed --bam received a bam file contains pooled reads, so I should merge all my individual bams into one bam?
@vibansal
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I don't think that merging bams will give good results. I would suggest running CRISP using pool size 2 and "--EM 0" option.

@vibansal vibansal closed this as completed Nov 4, 2022
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@vibansal @raksasa