I would like to know like GATK 3.6 there was an option to define active regions, is there any option in GATK v4.2.1
The Active region parameters can be seen from this link:-
https://software.broadinstitute.org/gatk/documentation/tooldocs/3.5- /org_broadinstitute_gatk_tools_walkers_diagnostics_FindCoveredIntervals.php.
- advanced input which has a parameter name --activeRegionIn,
If i correctly understand, this is the list of interval (can be in bed file) to define active regions which would be further used for phasing.
1) What is the similar parameter in the new GATK release?
2) Using new version of GATK, VCF files has only 2 rows out of ** 228 rows** that have PID information. How do i go in such a case. Have i done any mistake in my analysis .
My commands are as follows:-
/opt/apps/gatk/4.2.1/gatk Haome_analysis/reference/Homo_sapiens.GRCh37.dna.chromosome.6.fa -I base_recalib/abc_aligned_sorted_dupmarked_realigned_recalibrated.bam -O haplotype_caller/abc_haplotyper.g.vcf --emit-ref-confidence GVCF -L /home/dhwani.dholakia/archive/files_required_for_exome_analysis/coord.bed --max-assembly-region-size 1000 -mbq 25 -stand-call-conf 40