questions about VCF filtering

[d'Agata Léo]

Hi,

I have some other questions:

- I want to filter my VCF file according to the FILTER field (I keep when it's fixed to "PASS". But there are also the FORMAT field which contains FT field fixed on LowQual or PASS. Do I have to filter this field too?

- When creating my BAM file before give it to Delly, I filter it with the command "samtools view -Sb -F4" to remove that is unmapped. Does it have any impact to Delly for the Split-Reads analysis ?

- I didn't success to launch the script somaticFilter.py. I get the following error:

File /.../delly/variantFiltering/somaticVariants/somaticFilter.py", line 8, in <module>

    import vcf

ImportError: No module named vcf

Do you have any idea about this problem?  

 

Best,

Léo

[Tobias Rausch]

If you have only a single sample you might consider using FT. It's also better to keep all reads in the bam file.

For the python script you lack the PyVCF module.

-Tobias

[d'Agata Léo]

Thanks a lot!