vawk

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Parsing sample names as external variable are not recognized in the Sample field.

1

Given a multisample VCF file with different samples, if the sample name is given as a external variable, such as `sample_name="NA00001" ` ` zcat MULTI_VCF | vawk -v ext_var=$sample_name '{print...

acontrerasg

Is there a limit on the number of infofields to print? I was trying to print all the dbnsfp annotated info fields: getting below error ``` Traceback (most recent call...

gpcr

Enhancement request: I$* to print all INFO fields

1

I$* to print all INFO fields

gpcr

Still works with python2 and now works well with python3

florealcab

error with dbNSFP_GERP++ info fields

5

vawk '{print I$dbNSFP_GERP++_RS}' input vcf prints only 0 example line from vcf to test: 11 47353646 . C T . . dbNSFP_GERP++_RS=4.33;dbNSFP_GERP++_RS_rankscore=0.52;dbNSFP_phyloP46way_primate=-0.41;

gpcr

Allow user to rename the sample columns in the header.

cc2qe

VCF header missing = silent failure

6

If the VCF header is missing from the input data stream, `vawk` seems to silently fail when constructing an awk program.

mdshw5

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...

cc2qe

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...

cc2qe