Colby Chiang

We can calculate an estimate for PE/SR ratio based on the read length and insert size. SVs that deviate from this ratio (e.g. few or none of an evidence type)...

Allow user to rename the sample columns in the header.

python wrapper is slower than straight awk

7

``` time zcat Omni25_genotypes_2141_samples.b37.v2.vcf.gz | vawk --header '{ print $1,$2,$3,$4,$5,$6,$7,$8,$9,S$NA12878 }' | bgzip -c > NA12878.omni.vcf.gz # real 19m43.893s # user 21m27.138s # sys 0m59.355s # aside: outside python it's...

1. Bypass "if in header" statement after the top of file 2. Split INFO field by using multip grep, and moving the 'or' statement inside the loop (rather than many...