gravatar for vaibhash

3 hours ago by

Hi Team ...

I want to use bcftools, or any other non-hail way, to achieve below filtering on my vcf files ...

#filter for samples that are > 95% call rate

hail way

mt = mt.filter_cols(mt.sample_qc.call_rate >= 0.95)

I'm very new to the bioinformatics world and have used bcftools till now to do following tasks ...

  1. normalization of vcf files ( via norm option of bcftools )
  2. filtering samples from vcf file ( by passing -s and -S flags to view option of bcftools )
  3. basic column based filtering like, via filter -i 'FILTER=="PASS" || FILTER=="MONOALLELIC"'
  4. concatenating blocks of vcf files ( via concat option of bcftools )

Can anyone please help me to achieve filtering for samples that have 95% of call rate?

or at least break down the steps required to achieve it and I will try to decode the manual of bcftools to achieve those steps ..

I tried finding solution in already answered question but didn't find a solution ... if someone has bookmarked the solution then please share that ...

May be this would help others too who don't want to use hail for basic filtering ...

I would appreciate any help, any pointer ...

thanks team ...

ps : if someone know a good video lecture or course that walks through some example scenarios with bcftools then please do share ...

link

modified 2 hours ago

written
3 hours ago
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vaibhash0



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