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made the header smaller

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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 SAM format and rename the file to ""*idxbase*.alt". For GRCh38, this alignment is
available from the [BWA resource bundle for GRCh38][res]. 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: Construct the index:
```sh ```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 For short reads, the postprocessing script `bwa-postalt.js` runs at about the
same speed as BAM compression. 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: Construct the index:
```sh ```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 As of now, ALT mapping is done in two separate steps: BWA-MEM mapping and
postprocessing. 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 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*, 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 Nonetheless, postprocessing is recommended as it improves mapQ and gives more
information about ALT hits. information about ALT hits.
### Step 2: Postprocessing #### Step 2: Postprocessing
Postprocessing is done with a separate script `bwa-postalt.js`. It reads all 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 potential hits reported in the XA tag, lifts ALT hits to the chromosomal