From bef171f181534863b132639985d21d50f4b00d3e Mon Sep 17 00:00:00 2001 From: CarolinaPB Date: Thu, 28 Oct 2021 11:14:47 +0200 Subject: [PATCH] Update README.md --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 9e73104..b57128e 100644 --- a/README.md +++ b/README.md @@ -60,6 +60,10 @@ Tip: use the name of the bam file without the .bam extension as the sample name. - PREFIX - prefix for the created files - NUM_CHRS - number of chromosomes for your species (necessary for plink). ex: 38 - BWA_MEM_M - if you mapped your reads with `bwa mem` using the `-M` parameter and you want split read support in your VCF you need to run an extra step. For this write `Y`. + - If `BWA_MEM_M: Y` an extra step will be done: **split_disc_reads** to create the split and disc bam files before smoove call runs + - If `BWA_MEM_M: N` **split_disc_reads** will not run and the pipeline will start with the **smoove_call** step +For a more detailed explanation see [smoove SR support](https://carolinapb.github.io/2021-10-28-smoove-SR-support/) + If you want the results to be written to this directory (not to a new directory), comment out or remove ```