VCFtools indels/SNP treatment

Question

[draccident]

Hello Stars,

Does anyone happen to know what Vcftools v0.1.17 default treatment for "--remove-indels" is when there is a SNP positions that overlaps with it? Presumably, the "SNP" is not removed because it is not labeled as a indel...

If so, what are ways to ensure those "SNPs" are removed...

[Jeremy Leipzig]

I think you would really have to define your expected behavior explicitly.

What does it mean for an insertion and a substitution to "overlap"?

what if it the substitution overlaps with the indel in the same sample - one allele for each?

[draccident]

Say that you have INDEL starting at position 15 AGTAGTCATACATCAT

At position 19 you have a SNP G T

and at position 25 you have a SNP C G

Are those SNPs retained?

Answer 1

[Jeremy Leipzig]

##fileformat=VCFv4.0
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FILTER=<ID=q10,Description="Quality below 10">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  A   B
1   15  .   AGTAGTCATACATCAT    A   1806    q10 DP=35   GT:GQ:DP    1/1:409:35  1/1:409:35
1   19  .   G   T   1792    PASS    DP=32   GT:GQ:DP    0/0:245:32  0/0:245:32
1   25  .   C   G   628 q10 DP=21   GT:GQ:DP    0/1:245:32  0/1:245:32

run vcftools

vcftools --vcf subset.vcf --remove-indels --out SNPs_only --recode

cat SNPs_only.recode.vcf

##fileformat=VCFv4.0
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FILTER=<ID=q10,Description="Quality below 10">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  A       B
1       19      .       G       T       1792    PASS    .       GT:GQ:DP        0/0:99:32       0/0:99:32
1       25      .       C       G       628     q10     .       GT:GQ:DP        0/1:99:32       0/1:99:32

now try with an individual exhibiting both alleles. can it decompose these before the filter?

##fileformat=VCFv4.0
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FILTER=<ID=q10,Description="Quality below 10">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  A   B
1   15  .   A   G,AG    1806    q10 DP=35   GT:GQ:DP    0/1:409:35  1/1:409:35
1   25  .   C   G   628 q10 DP=21   GT:GQ:DP    0/1:245:32  0/1:245:32

nope

##fileformat=VCFv4.0
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FILTER=<ID=q10,Description="Quality below 10">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  A       B
1       25      .       C       G       628     q10     .       GT:GQ:DP        0/1:99:32       0/1:99:32