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Add documentation describing the output format of out.hla.* files (doc fix only) #39

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Add documentation describing the output format of out.hla.* files (doc fix only) #39

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6 changes: 5 additions & 1 deletion bwakit/README.md
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Expand Up @@ -40,6 +40,10 @@ The last mapping command line will generate the following files:

* `out.log.*`: bwa-mem, samblaster and HLA typing log files.

The format of `out.hla.top` and `out.hla.all` output files is TAB delimited with
each GT line consisting of allele1, allele2, #mismatches/gaps on primary exons, #mismatches/gaps
on other exons and #exons used in typing. If unsure, use the first GT line as the final genotype.

Bwakit can be [downloaded here][res]. It is only available to x86_64-linux. The
scripts in the package are available in the [bwa/bwakit][kit] directory.
Packaging is done manually for now.
Expand Down Expand Up @@ -74,7 +78,7 @@ bwa.kit
|-- README.md This README file.
|-- run-bwamem *Entry script* for the entire mapping pipeline.
|-- bwa *BWA binary*
|-- k8 Interpretor for *.js scripts.
|-- k8 Interpreter for *.js scripts.
|-- bwa-postalt.js Post-process alignments to ALT contigs/decoys/HLA genes.
|-- htsbox Used by run-bwamem for shuffling BAMs and BAM=>FASTQ.
|-- samblaster MarkDuplicates for reads from the same library. v0.1.20
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2 changes: 1 addition & 1 deletion bwakit/typeHLA.js
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Expand Up @@ -69,7 +69,7 @@ if (arguments.length == getopt.ind) {
print("");
print("Note: The output is TAB delimited with each GT line consisting of allele1, allele2,");
print(" #mismatches/gaps on primary exons, #mismatches/gaps on other exons and #exons");
print(" used in typing. If unusure, use the first GT line as the final genotype.\n");
print(" used in typing. If unsure, use the first GT line as the final genotype.\n");
exit(1);
}

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