Filter VCF file
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7.9 years ago
sukesh1411 ▴ 30

Hi

How do I filter the vcf file using below filters:

  1. number of reads per base is between 5 and 75
  2. base quality > or = to 30
  3. mapping quality >= 60
  4. variant quality >= 90
  5. distance of adjacent variant >= 5
snp next-gen • 3.4k views
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http://snpeff.sourceforge.net/SnpSift.html#filter

and it will be something like
cat variants.vcf | java -jar SnpSift.jar filter " ( QUAL >= 30 ) && ( (DP >= 5) && (DP <= 75))" > filtered.vcf

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Hi sir

Thank you for your reply. I would like to know what are terms used for mapping quality, variant quality and distance of adjacent variant in vcf file?

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Hi sir

Can i know whether these terminologies are correct ?

DP - no of reads per base QUAL - variant quality MQ - mapping quality BQ - base quality and i cudnt find terminology for distance of adjacent variant.

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Yes you are right from the header you can read

INFO=<id=dp,number=1,type=integer,description="total depth"="">

total number of sequence reads overlapping that position MQ : RMS mapping quality, similar to the version in the INFO field. (Integer) BQ : RMS base quality at this position
http://seqanswers.com/forums/showthread.php?t=9345

I cudnt find terminology for distance of adjacent variant

you mean between the reference and sample ?!

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Hi sir

Thank you for your reply. I could not find adjacent variant term in .vcf file.

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