/home/anaconda3/share/gatk4-18.104.22.168-0/gatk HaplotypeCaller --java-options -Xmx100g -R genome.fa -I fixed.bam -O NmMdAndUqTag_fixed.g.vcf.gz -ERC GVCF --minimum-mapping-quality 20 --min-base-quality-score 20
In my case, We had used the Target enrichment sequencing approach for European Bison. We had sequenced a specific chromosome, for example, Chr1, Chr 2, Chr 15, Chr 9 for a specific gene panel.
But When I check the results obtained using Haplotype Caller, I am getting variants (SNPs) for all chromosomes. I am very confused. Shouldn't We have Variant only on the specific Chromosome that I had mentioned above? I was mainly interested to get Variant on specific sequenced (Mentioned above) chromosomes.
Do we have any specific program or parameter in GATK to call variants within targeted regions?
I had tried to use -L Haplotype caller parameter also. I had created a file named "interval_list", where I had mentioned the regions that were used to sequence.
Chr "\t" Start Position "\t" End Position
But It didn't work for me.
Your suggestions would be extremely helpful.
Thank you so much in advance.
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