Entering edit mode
21 months ago
kk.mahsa
▴
150
Hi everyone
I used the following method to create a VCF file with 50 samples.
For each sample
java -jar gatk_3.7-0/GenomeAnalysisTK.jar -T HaplotypeCaller -R Ref.fasta -I input.bam -o output.g.vcf.gz -ERC GVCF
and then for all samples
java -Xmx64G -jar gatk_3.7-0/GenomeAnalysisTK.jar -T GenotypeGVCFs -R Ref.fasta -V output1.g.vcf.gz -V output2.g.vcf.gz ... output50.g.vcf.gz -o 50_samples.vcf.gz
But my final VCF file has 45 samples instead of 50 samples. I don't get any error messages.
Can anyone help me to solve this problem?
I ran your command on the 15 samples (Sam1 to Sam15) that the missing data belonged to them and the command output was:
what is that mean?
you only have 19 distinct samples in all your VCF. . My guess is that the original BAMs have the same samples. Check with
Thanks dear Pierre for your help; I checked the BAM files and realized that I made a mistake in adding the sample name to the BAM files and it is a duplicate name