How do I get single multianno.txt file for multiple samples from Annovar?
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23 months ago
pragnapcu ▴ 10

I have done GATK joint calling for multiple samples and got a single hardfiltered.vcf.

I annotated this vcf file using the following command and got multiple .avinput files (one for each sample)

convert2annovar.pl -format vcf4 hardfiltered.vcf -allsample -withzyg -outfile out.avinput -includeinfo

Annotation with table_annovar.pl would give me the output for each of the samples separately

perl table_annovar.pl out.sample1.avinput AnnovarDb out.sample2.avinput AnnovarDb -buildver hg38 -out Md -remove -otherinfo -protocol refGene, gnomad211_exome, 1000g2015aug_all, esp6500siv2_all, gnomad30_genome, kaviar_20150923, avsnp150,dbnsfp42a,dbscsnv11,intervar_20180118,revel, clinvar_20210501,genomicSuperDups, dgvMerged,gwasCatalog -operation gx,f,f,f,f,f,f,f,f,f,f,f,r,r,r  -nastring . -polish -xref gene_fullxref.txt

but, how can I get single multianno file with format (at the end) dedicated to each sample individually?

joint table_annovar.pl GATK Annovar typing • 545 views
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