Question

gVCF to VCF conversion - 1000 Genomes Project data

0

Entering edit mode

7.1 years ago

anu014 ▴ 190

Hello Biostars,

I want to use 1000 Genomes Project phase3 data. Is it possible to get gVCFs instead of VCFs ? If not, is there any way we can convert VCF to gVCFs??

Thank you in advance :)

sequencing SNP next-gen • 2.3k views

ADD COMMENT • link updated 7.1 years ago by WouterDeCoster 47k • written 7.1 years ago by anu014 ▴ 190

0

Entering edit mode

This thread asks about gVCFs -> VCFs, maybe there's some info there.

ADD REPLY • link 7.1 years ago by jonasmst ▴ 410

score 1 · Answer 1 · 2017-03-10

1

Entering edit mode

7.1 years ago

WouterDeCoster 47k

No, you cannot convert VCFs to gVCFs. Those files don't contain the required information for conversion. For getting the gvcf files you would have to repeat variant calling, starting from the bam file.

ADD COMMENT • link 7.1 years ago by WouterDeCoster 47k

0

Entering edit mode

Can you elaborate what is that extra information required?

ADD REPLY • link 7.1 years ago by anu014 ▴ 190

0

Entering edit mode

See the gvcf specifications.

ADD REPLY • link 7.1 years ago by WouterDeCoster 47k

0

Entering edit mode

Thank you for the help, I'll go through it :)

ADD REPLY • link 7.1 years ago by anu014 ▴ 190