Hi all, I have two objectives for my analysis:
- To find out denovo and rare variants from autism trios analysis
Trios: (Father, Mother, Proband)
- To detect frequently occuring mutation across autism patient.
I have used GATK best practice to identify the germline variants across 15 trios (
Total 45 samples [15X3]) and I have generated
gVCF file for all the 45 samples.
Can some one guide me how to call
de novo variants from this trios cohort?
Are there much difference between
GATKforum they appear to be similar for me.
Are you sure the analysis can not be carried out with
a gVCF can only handle one individual, so you couldn't use them call trios with tools that expect a trio VCF (correction: yes there are multi-sample gVCFs that briefly arise from CombineGVCFs but they are never found in the wild)
Are there any tools to convert gvcf to vcf file. I found another question here
They use following command
gzip -dc sample.genome.vcf.gz | extract_variants | bgzip -c > sample.vcf.gz
is it fine to do like this?
@ Pierre Lindenbaum
Hi @Pierre Lindenbaum, I used following command to generate the vcf files. Is it correct to call the vcf files this way
Variant calling using Haplotype caller algorithm
Calling only variants from a Genome VCF file
no you first need to call CombineGVCFs for all your samples and then GenotypeGVCFs
Can you clarify my doubt ? there are
proband. (15*3=45 files)
How I need to combine the
Combine all 45
Combine 15 proband's
gvcfof single trios, similarly for all 15 trios separately ?
combine ALL files.
@Pierre Lindenbaum, I appreciate your help
Hi, I tried combinegvcf followed by GenotypeGVCFs
It gave me an output like this,
How do I call denovo variants from each trio set here?
see my answer. I told you to use
May I know whether the pedigree file which I created is correct?
Ya, this format is correct, but you need to add
#in the first line as:
why don't you just try to use it ?