Filter VCF file

Question

[sukesh1411]

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

[Medhat]

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

[sukesh1411]

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?

[Medhat]

Do you mean information about vcf specification?

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40/

http://samtools.github.io/hts-specs/VCFv4.2.pdf

[sukesh1411]

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.

[Medhat]

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 ?!

[sukesh1411]

Hi sir

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