Changes between Version 14 and Version 15 of SOPs/variant_calling_GATK
- Timestamp:
- 07/13/15 11:51:01 (10 years ago)
Legend:
- Unmodified
- Added
- Removed
- Modified
-
SOPs/variant_calling_GATK
v14 v15 3 3 4 4 This information comes from the [[http://www.broadinstitute.org/gatk/guide/events?id=3093#materials|slides for "Best Practices for Variant Calling with the GATK"]] from the Broad Institute. This page summarizes and formats their detailed documentation. 5 \\ \\ 6 Note that if you're calling variants from RNA-seq reads, follow the somewhat different commands optimized for this, as described in GATK's [[https://www.broadinstitute.org/gatk/guide/article?id=3891|Calling variants in RNAseq]]. 5 7 \\ \\ 6 8 This example pipeline starts with a single-end short-read fastq file (Reads_1.fq).
