How to extract postions from gnomad using tabix?

Question

[DareDevil]

Hi I have list of positions around 2 lakhs and I want to map those regions in gnomad. I tested for one postion uisng tabix. But it extracts other positions as well.

tabix af-only-gnomad.hg38.vcf.gz chr1:10217-10217

output

chr1    10114   .       TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T       36729   PASS    AC=9,1;AF=0.0002246,2.496e-05
chr1    10211   .       AACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACCCT A       6206.06 PASS    AC=2;AF=5.319e-05
chr1    10217   .       A       T       20051.80        PASS    AC=2;AF=5.288e-05

but I need only following as ouput. Where am I doing wrong?

chr1    10217   .   A   T   20051.80    PASS    AC=2;AF=5.288e-05

[tothepoint]

Can you check if tabix af-only-gnomad.hg38.vcf.gz "chr1:10217-10217" works.

[DareDevil]

I tried the same, but does not work

[tothepoint]

I just cross checked and this works smoothly. Can you again perform bgzip and tabix to check if indexing was performed accordingly.

[DareDevil]

I have done bgzip af-only-gnomad.hg38.vcf followed by tabix -p vcf af-only-gnomad.hg38.vcf.gz. Then,

tabix af-only-gnomad.hg38.vcf.gz "chr1:10217-10217"

output:

chr1    10114   .   TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA  CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T    36729   PASS    AC=9,1;AF=0.0002246,2.496e-05
chr1    10211   .   AACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACCCT  A   6206.06 PASS    AC=2;AF=5.319e-05
chr1    10217   .   A   T   20051.80    PASS    AC=2;AF=5.288e-05

Answer 1

[Pierre Lindenbaum]

tabix is right

for example the 1st variant.

chr1    10114   .       TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T       36729   PASS    AC=9,1;AF=0.0002246,2.496e-05

would overlap "chr1:10217-10217" because the first variant starts at 10114 and ends at 10114+length(REF) = 10398. So chr1:10114-10398 overlaps your query chr1:10217-10217

you could use bcftools view --types snps gnomad.vcf.gz chr1:10217-10217

[DareDevil]

perfect !!!!... thanks :)

[tothepoint]

Dear Sir, Thankyou so much.