HaplotypeCaller on defined set of SNPs
I have a set of sequenced PCR amplicons in bam files (one per samples) where I need to call defined SNP positions to get a combined genotype, no matter if it is reference or alternative homozygous or heterozygous.
I am running the following commands:
java -jar GATK/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R $1 \
-I $f \
-o $out.vcf \
--dbsnp workspace/vcforiginal.vcf \
-ERC BP_RESOLUTION \
-L projects/ION-Analysis-files/TSAncestryPanel/PrecisionID_AncestryPanel_hotspots.bed \
--downsampling_type none \
--genotyping_mode DISCOVERY \
Here my three questions:
1) Any idea why it is unable to update the index for the .vcf file ? Generally, why would it want to do that ?
Done. There were 3 WARN messages, the first 3 are repeated below.
WARN 11:32:04,723 RMDTrackBuilder - Unable to update index with the sequence dictionary for file /home/GMI/q023me/workspace/vcforiginal.vcf.idx; this will not affect your run of the GATK
WARN 11:32:04,946 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
WARN 11:32:05,440 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not org.broadinstitute.gatk.tools.walke
The results file shows the dbSNP annotation only for heterozygous calls, any way I can change this to show it for all positions ?
Would -ERC BP_RESOLUTION be the most appropriate option ? Why can I not use genotype_given_allels option with this ? (I know I'm missing a point here)
Thank you in advance and kind regards,