Filtering MToolBox VCF

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Roberto Preste edited this page Nov 16, 2019 · 2 revisions

AUXILIARY SCRIPTS FOR DEALING WITH MTOOLBOX DATA

These are found in the MToolbox aux folder.

get_prioritized_var_and_summary.sh is an auxiliary script can be used to get the summary.txt and prioritized_variant.txt files from the MToolBox annotation.csv files.

Run this to get help on script usage:
```
./get_prioritized_var_and_summary.sh
```
filter_HF.py is an auxiliary script to filter MToolBox VCF files (generated by versions < 1.2) for HF and DP and split multiallelic SNP into one per row.

Run this to get help on script usage:
```
python filter_HF.py 
```
filter_HF_v2.py is an auxiliary script to filter MToolBox VCF files (generated by versions >= 1.2) for HF and DP and split multiallelic SNP into one per row.

Run this to get help on script usage:
```
python filter_HF_2.py
```
Usage examples:
```
python filter_HF_v2.py HG00119 HG00119.vcf 0.8 100 txt HG00119.txt No
```
Expected content of the HG00119.txt output:

CHROM POS ID REF ALT DP HF CIL CIU SDP_F SDP_R HG00119

chrMT 73 . A G 246.0 1.0 0.981 1.0 117 129 HG00119

chrMT 195 . T C 234.0 1.0 0.981 1.0 67 167 HG00119