Problem with VCF filtering

[Louis Gauthier]

Hi Melissa,

I'm using lobSTR on WGS Illumina data. I've successfully allelotyped my files and I'm now trying to filter the resulting VCFs.

Using the filtering script yields the following error:

Traceback (most recent call last):

  File "lobSTR_filter_vcf.py", line 161, in <module>

    if LogScore(sample["Q"]) < args.call_log_score:

  File "lobSTR_filter_vcf.py", line 33, in LogScore

    return -1*math.log10(1-score+SMALLNUM)

TypeError: unsupported operand type(s) for -: 'int' and 'NoneType'

Now this error is obviously thrown because my VCFs contain genotypes for which no call has been made (GT field is './.'), causing the variable 'score' to be set to 'None'.

Since the VCFs have been generated by lobSTR and I assume it logical that there would be at least some positions without a call, is it possible this might just be a missing verification in the code? i.e. check if a call has been made before trying to parse info for each field.

I wrote a working quick fix to debug the problem but I wouldn't want to mess with the code too much as I'm no python expert.

Everything else has been running (almost) flawlessly so far. Thanks in advance!

Louis 

[CoCo]

if sample["GT"]: -> if sample["GT"] != "./." :

[Irene L]

Thanks, this solved my problem!

[takic...@gmail.com]

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