Hello, I use GATK 4.1.6.0 (and I am still newcomer to bioinformatics). I want to make gemini import of combined (trio) vcf and apply PED file to establish pedigree. All of the three vcfs indicate sample name as "20", defined in "FORMAT 20" tag. Therefore gemini import announces "ValueError: Sample 20 found in the VCF but not in the PED file". I would like to have samples defined by input file names (in my case SM085, SM086, SM087). I am confused where the sample name "20" originates from as I do not use it in my scripts. I would like to ask in which step of the GATK pipeline I am able to input pedigree/sample names. Thank you.
1 answer
I would like to ask in which step of the GATK pipeline I am able to input pedigree/sample names. Thank you.
if the VCF were created with GATK (HaplotypeCaller), the software use the read groups in the BAM files. See : Read Group In Sam/Bam Files: What Do They Exactly Describe?
Read groups are defined when mapping the FASTQ on a reference genome with bwa for example with option -R
if all your BAMs have a read group like
@RG ID:12345 SM:20
all your VCFs will have a sample named '20'
you can rename your VCF with bcftools reheader
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