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.
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.
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