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merged gff2bed and mapstat to paftools

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Heng Li
2018-02-09 10:47:12 -05:00
parent 3465b04724
commit 2025a6279a
5 changed files with 271 additions and 529 deletions
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misc/README.md
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@@ -125,7 +125,7 @@ k8 ov-eval.js reads-to-ref.paf ovlp.paf
## <a name="asmvar"></a>Calling Variants from Haploid Assemblies
Script [paf2diff.js](paf2diff.js) calls variants from coordinate-sorted
Command `paftools.js call` calls variants from coordinate-sorted
assembly-to-reference alignment. It calls variants from the [cs tag][cs] and
identifies confident/callable regions as those covered by exactly one contig.
Here are example command lines:
@@ -133,7 +133,7 @@ Here are example command lines:
```sh
minimap2 -cx asm5 -t8 --cs ref.fa asm.fa > asm.paf # keeping this file is recommended; --cs required!
sort -k6,6 -k8,8n asm.paf > asm.srt.paf # sort by reference start coordinate
k8 paf2diff.js asm.srt.paf > asm.var.txt
k8 paftools.js call asm.srt.paf > asm.var.txt
```
Here is sample output: