Problem with annovar in GATK4 output
Hello
Based on GATK4 best practices pipline I have made a VCF file composed 4 person WES data. When I want to annotate it with annovar , but annovar could not annotate all variations and near 70% of variations discard and gone to Invalid_input.
I though it might happen due to VCF version (4.2), but it doesn't work with annovar default input format (avinput).
What is your suggestion for annotating GATK4 output VCFs?
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ahmad mousavi
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Please paste some of the variants that are stored in invalid_input
A better approach may be to first split your variants into 4 different avinput files, and then annotate these:
thanks for reply. The problems still exist. I have 5 sample ( output from Haplotypecaller which merged by Bcftools), but after running you command each file is separated and it is hard to track a SNP in all 5 samples.
Can I annotate all 5 samples individually and then merge annotated result into one file?
It gives following information, I lost almost 50,000 SNPs and indels
Without seeing your VCF, I cannot understand entirely what is going on. The only filter that could result in substantial loss of variants is the
--snpqual <float>filter passed to convert2annovar.pl, with an initial value set to 20.Other possibilities to consider:
You could indeed process each sample independently with the
--allsampleflag, and then merge it all back together. You should keep rack of wich variants were called in which individual, though. When sample number is low, I believe that doing it this way is fine.