Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
FastQC showed me my raw data has 2 peaks in the GC content tab
I just got my FFPE samples back from the sequence provider, I see a double peak like in the image, what does it mean? Should I be worried? Is this normal for FFPE samples? It was a single pair of normal/tumor samples.
Also, the fastQs for my matched normal is so much smaller at ~8GB than my tumor data ~40GB.
Here's the basic stats from the bam file after alignment and duplicate marking:
47803854 + 0 in total (QC-passed reads + QC-failed reads)
20972021 + 0 duplicates
24883875 + 0 mapped (52.05%:-nan%)
47803854 + 0 paired in sequencing
23901927 + 0 read1
23901927 + 0 read2
20554832 + 0 properly paired (43.00%:-nan%)
23992038 + 0 with itself and mate mapped
891837 + 0 singletons (1.87%:-nan%)
40520 + 0 with mate mapped to a different chr
32160 + 0 with mate mapped to a different chr (mapQ>=5)
212511606 + 0 in total (QC-passed reads + QC-failed reads)
22840440 + 0 duplicates
62720862 + 0 mapped (29.51%:-nan%)
212511606 + 0 paired in sequencing
106255803 + 0 read1
106255803 + 0 read2
43991506 + 0 properly paired (20.70%:-nan%)
58253560 + 0 with itself and mate mapped
4467302 + 0 singletons (2.10%:-nan%)
116068 + 0 with mate mapped to a different chr
77003 + 0 with mate mapped to a different chr (mapQ>=5)
Will my downstream analysis be okay? I'd appreciate any advice.