# Which vcf to use for tumor calls? (neuroblastoma)

**URL:** <https://forum.kidsfirstdrc.org/t/which-vcf-to-use-for-tumor-calls-neuroblastoma/97>\
**Category:** Data Access & Analysis\
**Created:** [May 14, 2021, 3:54pm UTC](https://forum.kidsfirstdrc.org/t/which-vcf-to-use-for-tumor-calls-neuroblastoma/97 "2021-05-14T15:54:34Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![rdmelamed](https://avatars.discourse-cdn.com/v4/letter/r/22d042/32.png) [@rdmelamed](https://forum.kidsfirstdrc.org/u/rdmelamed)\
**Post date:** [May 14, 2021, 3:54pm UTC](https://forum.kidsfirstdrc.org/t/which-vcf-to-use-for-tumor-calls-neuroblastoma/97/1 "2021-05-14T15:54:34Z")

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Hello!  
I’m actually wondering more generally if there’s documentation about what the various files are and what purposes they are intended for.  
But specifically, if I want to get all high quality tumor variant calls, what would be the best file to use? I’ve been looking at the data for one patient PT\_YYGH8EMR. I was thinking that the somatic mutations found in the file `2114e40c-4db8-430e-a6c8-203f068037b2.consensus_somatic.PASS.vep.vcf.gz` should be a subset of all the variants found in `SL264139.hard-filtered.vcf.gz` but it does not seem to be true. Out of 24 consensus somatic variants on Chr 21, only 2 are in the hard-filtered file.

So, what is the hard-filtered file useful for? Can I use it for my purpose of getting the tumor calls, or must I start from the bam or fastq? I’d really rather not spend a ton of money running these pipelines when it seems like this must have already been done.  
Thank you!  
Rachel