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Are filtering and trimming necessary before mapping and SNP calling using GATK
Hi GATK team,
I am using GATK to call SNPs from whole genome re-sequencing data. According to FastQC report, base quality was lower than 20 after 100bp (120bp reads) and illumine Universal Adapter contents reach to 5% after 60 bp. I set base quality 30 and map quality 30 (--min_base_quality_score 30 --min_mapping_quality_score 30) to call SNP in GATK. Are these two settings enough to remove low quality data? Shall I need to remove reads with adapter contamination and trim low quality reads before mapping and SNP calling? Thanks very much for your help.
Here attached FastQC report