fixmate before/after GATK

[caswater]

Hello, everyone

I was just thinking if it would be better if I do a pre-processing for the aligned reads before sending it to GATK for SNP calling. For example, do I need to remove the unmapped and not properly paired reads, and run a fix mate for the bwa aligned files, and then send the processed bam files to GATK. Or GATK will take care of these issues automatically? Thank you for your advice.

one more question is ... after realignment by GATK, shall I run a fixmate before going to GATK recalibration?

Thank you for your kind advice!

[Jon_Keats]

If you are using a current version of GATK fixmate is no longer needed as it is done on the fly during indel realignment. There is no reason to remove the unmapped reads as they are not used for SNP calling, properly paired maybe a different issue but not a group of reads most people eliminate.

[caswater]

thank you... your advice really helps!!