How to only show SNPs in vcf files

Question

[Joe]

I have some vcf file generated by using GATK Unified Genotyper (--output_mode EMIT_ALL_SITES), it looks like

chr15 21138918 . C . 46.23 . . GT:DP 0/0:6

chr15 21138919 . C . 46.23 . . GT:DP 0/0:6

chr15 21138920 . T . 46.23 . . GT:DP 0/0:6

chr15 21138921 . C . 46.23 . . GT:DP 0/0:6

chr15 21138922 . A . 46.23 . . GT:DP 0/0:6

chr15 21138923 . A . 46.23 . . GT:DP 0/0:6

chr15 21138924 rs116806596 C T 173.84 . . GT:AD:DP:GQ:PL 1/1:0,6:6:18:202,18,0 chr15 21138925 . T . 43.23 . . GT:DP 0/0:6

chr15 21138926 . G . 46.23 . . GT:DP 0/0:6

chr15 21170494 . T . 34.23 . . GT:DP 0/0:5

chr15 21170495 . G . 34.23 . . GT:DP 0/0:5

chr15 21170496 . A . 34.23 . . GT:DP 0/0:5

My question is: Is there bcftools or vcftools could simply filter this vcf file to only show SNPs (eg, chr15 21138924 rs116806596 C T 173.84 . . GT:AD:DP:GQ:PL 1/1:0,6:6:18:202,18,0)?

I know that I can rerun GATK Unified Genotyper by using EMIT_VARIANTS_ONLY, but I have so many files, it is very time consuming.

Thanks.

[cpad0112]

java -jar  SnpSift.jar  filter --inverse  "( ALT = '.')" test.vcf.gz

Will work with vcf too. Last lines from output:

##SnpSiftVersion="SnpSift 4.3p (build 2017-06-06 09:55), by Pablo Cingolani"
##SnpSiftCmd=""
##FILTER=<ID=SnpSift,Description="SnpSift 4.3p (build 2017-06-06 09:55), by Pablo Cingolani, Expression used: ( ALT = '.')">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA00001
chr15   21138924    rs116806596 C   T   173.84  .   .   GT:AD:DP:GQ:PL  1/1:0,6:6:18:202,18,0

[Joe]

It works! Thanks a lot.

Answer 1

[Pierre Lindenbaum]

for F in *.vcf; do  awk  -F '\t' '($0 ~ /^#/ || $5!=".")' $F  > ${F}.2.vcf ; done