Hello, I am a new user of GATK and have a simple question here. I wish to call SNPs from one sample, and I was just wondering if I need to process and clean the aligned files by myself before having it as input of GATK.
First, basically I will use BWA to do the alignment for the FASTQ files - for the alignment parameters, shall I use "-q 20" to trim the reads with base quality scores lower than 20? or shall I just keep it as it is, and GATK will consider all the low-quality bases in its SNP calling?
Second, with the alignment file, shall I use "samtools view -q 1 ...." to remove those un-uniquely mapped reads? or shall I just need to directly re-align,recalibrate and remove duplicate, and then send it to GATK for SNP calling. I was just wondering normally do we need to do some filtering by ourselves using samtools?
Thank you very much for your kind response
First, basically I will use BWA to do the alignment for the FASTQ files - for the alignment parameters, shall I use "-q 20" to trim the reads with base quality scores lower than 20? or shall I just keep it as it is, and GATK will consider all the low-quality bases in its SNP calling?
Second, with the alignment file, shall I use "samtools view -q 1 ...." to remove those un-uniquely mapped reads? or shall I just need to directly re-align,recalibrate and remove duplicate, and then send it to GATK for SNP calling. I was just wondering normally do we need to do some filtering by ourselves using samtools?
Thank you very much for your kind response