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made the header smaller

This commit is contained in:
Heng Li 2014-10-16 17:17:02 -04:00
parent fab1f2b561
commit 67c2d69218
1 changed files with 4 additions and 4 deletions
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README-alt.md
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@ -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