Quick Start

Please follow the three steps below to generate your ATAV command:

1. Choose function: 2. Choose filters:

All Genotype Analysis Functions support all above filter options.
All Variant Annotation Functions support Variant and Annotation Level filter options.
All Coverage Analysis Functions and External datasets functions does NOT support above options.
Most functions its have own sub options.

Recommended filters for genotype analysis functions:

--exclude-artifacts --exclude-evs-qc-failed --min-coverage 10 --qd 2 --mq 40 --gq 20 --qual 30 --var-status pass+intermediate

3. Create sample file:
  • Search samples with AvaiContUsed = 'yes' from Sequence then create your sample file.

file header: Family ID, Individual ID, Paternal ID, Maternal ID, Sex, Phenotype, Sample Type, Capture Kit (tab delimited)

Family ID: specify a family id or use the same value as Individual ID to indicate this sample used as a non family control or case
Individual ID: sample name
Paternal ID: sample name (father) or 0 (indicate not available)
Maternal ID: sample name (mother) or 0 (indicate not available)
Sex: 1=male,2=female
Phenotype: 1=control, 2=case
Sample Type & Capture Kit: please use the value form seqdb, including “N/A” for genome samples
Ex. /nfs/goldstein/software/atav_home/data/sample/ALS_1424_DukeGr_ctrl.txt

Note: please make sure all the controls are approved to use in your input sample file.

4. Output:

--out /myworkspace/atav_output

5. Submit to Clusert:
  • It is required to submit all your ATAV jobs to our SGE cluster, more details please check: SGE Cluster Guide

6. Example Command:

qsub /nfs/goldstein/software/sh/atav.sh \
--list-var-geno \
--sample /nfs/goldstein/software/atav_home/data/sample/ALS_1424_DukeGr_ctrl.txt \
--function /nfs/goldstein/software/atav_home/data/function/functional.txt \
--gene TBK1 \
--ctrl-maf 0.01 \
--min-coverage 10 \
--out ~/hello_atav