GATK excludes some samples for cohort variant calling

[liu_xt005]

I used GATK to call variants from 20 exome-seq samples (one BAM file each sample). It excludes 4 among the 20. Anyone has a good solution? Thanks a lot.

The SAM files were generated by BWA with -r option, Picard was used to generate BAM, then local realignment, dedup, recalibration were done. Individual variant calling was totally fine, but does not give ref-homozygous genotype so that it is hard to differentiate ref-homozygous or missing genoype due to low coverage.

[liu_xt005]

My command line was:

java -Xmx4g -jar ~/GenomeAnalysisTK-1.1-37/GenomeAnalysisTK.jar \
-T UnifiedGenotyper -glm BOTH -nt 8 \
-R ~/hg18.fa \
-I sample01.bam -I sample02.bam -I sample03.bam -I sample04.bam -I sample05.bam \
-I sample06.bam -I sample07.bam -I sample08.bam -I sample09.bam -I sample10.bam \
-I sample11.bam -I sample12.bam -I sample13.bam -I sample14.bam -I sample15.bam \
-I sample16.bam -I sample17.bam -I sample18.bam -I sample19.bam -I sample20.bam \
-L ~/hg18_exonp10Intervals.bed \
-B:dbsnp,vcf ~/dbsnp_132.hg18.vcf \
-stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 100 -l INFO \
-A AlleleBalance -A DepthOfCoverage -A FisherStrand \
-log rawvariants.log \
-o rawvariants.vcf

Shall I assign more memory?

[liu_xt005]

It seems to be due to some RG tag errors. Already solved. Thanks!