diff --git a/bwakit/README.md b/bwakit/README.md index b7a67eaa..462d4d42 100644 --- a/bwakit/README.md +++ b/bwakit/README.md @@ -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. @@ -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 diff --git a/bwakit/typeHLA.js b/bwakit/typeHLA.js index b265d07d..258ddb6a 100644 --- a/bwakit/typeHLA.js +++ b/bwakit/typeHLA.js @@ -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); }