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Revision as of 16:25, 12 December 2014
, 16:25, 12 December 2014→Exonic Variants NOT found by 1000G
For example,
For example,
zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" | perl -lane 'print "$1\t$F[6]" if ( /ANNO=([^;:]+)/)' | sort | uniq -c
zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" | perl -lane 'print "$1\t$F[6]" if ( /ANNO=([^;:]+)/)' | sort | uniq -c
will give you the counts of variants, separate by the filtering results
will give you the counts of variants, separate by the filtering results
* Q2. Looking at each functional category, which functional categories has largest fraction of SNPs failed filter? Why do you think it is?
* Q2. Looking at each functional category, which functional categories has largest fraction of SNPs failed filter? Why do you think it is?
* Q3. Can you exclude the sites that are also in dbSNP, and count how many nonsense variants are left?
* Q3. Can you exclude the sites that are also in dbSNP, and count how many nonsense variants are left?
To also exclude those in dbsnp:
zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" | grep -v rs| perl -lane 'print "$1\t$F[6]" if ( /ANNO=([^;:]+)/)' | sort | uniq -c
Look at Stop_Gain variants
zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" |grep -v rs | perl -lane 'print "$_" if ( /ANNO=Stop_Gain/)' |grep -w PASS
If you want to know predicted functional significance of a particular variant, you can search by
If you want to know predicted functional significance of a particular variant, you can search by
