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Hi,
i have created several bam files from illumina-reads (paired-end), some (3) bam-files show a coverage of around 14, some (10) bam-files with a coverage around 6. I want to use UnifiedGenotyper from GATK for SNP calling but I am unsure on how to set the QUAL threshold, as it is described to use QUAL>= 4 for coverage smaller than 10x and QUAL>=30 for a coverage of at leasat 10x. I want to do multi-sample SNPcalling with QUAL>=30, but I m not sure if I`m to hard, regarding low coverage .bams. When I use QUAL>=4 i will call several of false-positive SNPs in the high-coverage bams...
Volavii
i have created several bam files from illumina-reads (paired-end), some (3) bam-files show a coverage of around 14, some (10) bam-files with a coverage around 6. I want to use UnifiedGenotyper from GATK for SNP calling but I am unsure on how to set the QUAL threshold, as it is described to use QUAL>= 4 for coverage smaller than 10x and QUAL>=30 for a coverage of at leasat 10x. I want to do multi-sample SNPcalling with QUAL>=30, but I m not sure if I`m to hard, regarding low coverage .bams. When I use QUAL>=4 i will call several of false-positive SNPs in the high-coverage bams...
Volavii