Merging BAM or VCF files, whats the difference?
Hello everybody.
I have two main set of file to analyze, the end goal is SNP discovery and haplotype for posterior imputation.
One dataset is haploid the other is diploid. I will investigate each separatelly
For each dataset I have shallow sequenced DNA 26 individual trees.
My question is; there is any practical implication on doing the Variant calling for each individual then merge into a big vcf rather then merge all alignemnts in one big .bam (RG for each individual) and then do the variant call.
As far as I can see the differences in the individual call will be relativized by mergevcf tool, no?
Thanks in advance.
• 2,045 views
•
link
written
by
leonardo.rippel •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
best practice for diploid variant calling
written by Matteo Ungaro •
-
Best practice to merge per sample variant calls from personalized pangenomes
written by Tobias •
-
Searching for tool to assign data as haploid or diploid
written by Naomi •
-
Combine haploid fastq's into diploid "individuals"
written by timothy.delory •
-
How to build a truth set
written by leonardo.rippel •
-
Imputating individual haplotype phase w/o Plink
written by los •
-
How to get a fake diploid sequence(each one from a population)
written by jinzheng9406 •
-
What kind of sequences I have, haploid or diploid?
written by Enrique López •
-
Diploid vs Haploid calls
written by Ghani •
-
Ancient DNA best practise
written by dilawerkh4 •
In my experience, I've always kept single bam files and performed joint genotyping with GATK for this task! I think it's safer for latter purposes.
So, obtaining a vcf for each sample and performing the joint genotyping with GATK. The thing is i'm not using GATK. I'm analysing the variants using DeepVariant. and I'm not sure if there is the same option. However I will keep in mind your solution.