VariantRecalibration step issue
Hi all, i need some advice about VariantRecalibration as in if I am doing the right thing?
Downloaded 30 bams from 1000 genomes and realigned them to HG38. Then using HaplotypeCaller generated a gVCF for each BAM. Then used CombineGVCFs and made a single VCF named cohort.g.vcf
Took a sample BAM and aligned to HG38. Then used HaplotypeCaller like above and generated a gVCF.
Now I am trying to genotype both the gVCFs using
java -Xmx16g -jar algorithms/gatk3/gatk3.8.jar -T GenotypeGVCFs -R references/hg38gatkbundle/Homo_sapiens_assembly38.fasta --variant data/HG100/HG100.output.raw.snps.indels.g.vcf --variant references/hg38gatkbundle/exomerefs/vcf/cohort.g.vcf -o data/HG100/output.raw.combined.vcf
This is not working. When I ran ValidateVCF from GATK, for my sample VCF i got message about --reference_window_size adjustment as in make it larger than 108, 170 etc. Then reran haplotype caller with --set_window_size 1000 but there is no change, same validation message.
ValidateVariants on the cohort.g.vcf reports a broken line.
I am not just not sure why these issues arise.
Is there a simple straightforward pipeline/ tutorial published somewhere that helps get over this issue?
Any help will be highly appreciated.