From 67c2d69218dcaae81b1d7c66a1b8d63dab0a5c5b Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 16 Oct 2014 17:17:02 -0400 Subject: [PATCH] made the header smaller --- README-alt.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README-alt.md b/README-alt.md index 7a578f9..8dac185 100644 --- a/README-alt.md +++ b/README-alt.md @@ -6,7 +6,7 @@ ALT-aware mode, users need to provide pairwise ALT-to-reference alignment in the SAM format and rename the file to ""*idxbase*.alt". For GRCh38, this alignment is available from the [BWA resource bundle for GRCh38][res]. -### Option 1: Mapping to the official GRCh38 with ALT contigs +#### Option 1: Mapping to the official GRCh38 with ALT contigs Construct the index: ```sh @@ -27,7 +27,7 @@ bwa mem hs38a.fa read1.fq read2.fq \ For short reads, the postprocessing script `bwa-postalt.js` runs at about the same speed as BAM compression. -### Option 2: Mapping to the collection of GRCh38, decoy and HLA genes +#### Option 2: Mapping to the collection of GRCh38, decoy and HLA genes Construct the index: ```sh @@ -68,7 +68,7 @@ implementation encourages researchers to use ALT contigs soon and often. As of now, ALT mapping is done in two separate steps: BWA-MEM mapping and postprocessing. -### Step 1: BWA-MEM mapping +#### Step 1: BWA-MEM mapping At this step, BWA-MEM reads the ALT contig names from "*idxbase*.alt", ignoring the ALT-to-ref alignment, and labels a potential hit as *ALT* or *non-ALT*, @@ -92,7 +92,7 @@ If we don't care about ALT hits, we may actually skip postprocessing (step 2). Nonetheless, postprocessing is recommended as it improves mapQ and gives more information about ALT hits. -### Step 2: Postprocessing +#### Step 2: Postprocessing Postprocessing is done with a separate script `bwa-postalt.js`. It reads all potential hits reported in the XA tag, lifts ALT hits to the chromosomal