lordzappo/basicfiltering

Basic filtering scripts for various mutation calling tools

basicfiltering

Basic Filtering for:

1. Variant Allele Frequency = 1% (default)
2. Variant Reads = 5 (default)
3. Tumor-Normal Variant Allele Frequency Ratio >= 5 (default)
4. If vcf of hotspot location are given it skips positions that have hotspots regardless of not satisfying number 3 from the above criteria

for Multiple Tools

Requirements:

• pyvcf : v0.6.7
• pandas : v0.16.2
• nose : v1.3.7

Auto CWL post-process requirements

• Convert inputVcf to have both string and file as input type
• Convert inputTxt to have both string and file as input type
• Convert hotspotVcf to have both string and file as input type

Works with following versions output formats:

SomaticIndelDetector (filter_sid.py)

• SomaticIndelDetector in GATK version = 2.3-9
• Takes in the text and vcf file input and filters based on text input.

usage: filter_sid.py [options]

Filter Indels from the output of SomaticIndelDetector

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         make lots of noise
  -ivcf SomeID.vcf, -inputVcf SomeID.vcf
                        Input SomaticIndelDetector vcf file which needs to be
                        filtered
  -itxt SomeID.txt, -inputTxt SomeID.txt
                        Input SomaticIndelDetector txt file which needs to be
                        filtered
  -tsn SomeName, --tsampleName SomeName
                        Name of the tumor Sample
  -dp 0, --totaldepth 0
                        Tumor total depth threshold
  -ad 5, --alleledepth 5
                        Tumor allele depth threshold
  -tnr 5, --tnRatio 5   Tumor-Normal variant frequency ratio threshold
  -vf 0.01, --variantfrequency 0.01
                        Tumor variant frequency threshold
  -hvcf hostpot.vcf, --hotspotVcf hostpot.vcf
                        Input bgzip / tabix indexed hotspot vcf file to used
                        for filtering
  -o /somepath/output, --outDir /somepath/output
                        Full Path to the output dir.

MuTect (filter_mutect.py)

• MuTect version = 1.1.4
• Takes in the text and vcf file input and filters based on text input.

usage: filter_mutect.py [options]

Filter SNPS from the output of muTect v1.14

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         make lots of noise
  -ivcf SomeID.vcf, -inputVcf SomeID.vcf
                        Input vcf muTect file which needs to be filtered
  -itxt SomeID.txt, -inputTxt SomeID.txt
                        Input txt muTect file which needs to be filtered
  -tsn SomeName, --tsampleName SomeName
                        Name of the tumor Sample
  -dp 0, --totaldepth 0
                        Tumor total depth threshold
  -ad 5, --alleledepth 5
                        Tumor allele depth threshold
  -tnr 5, --tnRatio 5   Tumor-Normal variant frequency ratio threshold
  -vf 0.01, --variantfrequency 0.01
                        Tumor variant frequency threshold
  -hvcf hostpot.vcf, --hotspotVcf hostpot.vcf
                        Input bgzip / tabix indexed hotspot vcf file to used
                        for filtering
  -o /somepath/output, --outDir /somepath/output
                        Full Path to the output dir.

VarDict (filter_vardict.py)

• VarDict version = 1.4.6
• Takes in a vcf and filters based on it

usage: filter_vardict.py [options]

Filter Indels from the output of vardict

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         make lots of noise
  -i SomeID.vcf, -inputVcf SomeID.vcf
                        Input vcf vardict file which needs to be filtered
  -tsn SomeName, --tsampleName SomeName
                        Name of the tumor Sample
  -dp 0, --totaldepth 0
                        Tumor total depth threshold
  -ad 5, --alleledepth 5
                        Tumor allele depth threshold
  -tnr 5, --tnRatio 5   Tumor-Normal variant frequency ratio threshold
  -vf 0.01, --variantfrequency 0.01
                        Tumor variant frequency threshold
  -hvcf hostpot.vcf, --hotspotVcf hostpot.vcf
                        Input bgzip / tabix indexed hotspot vcf file to used
                        for filtering
  -o /somepath/output, --outDir /somepath/output
                        Full Path to the output dir.

PINDEL (filter_pindel.py)

• PINDEL version = 0.2.5a7
• Takes in a vcf and filters based on it

usage: filter_pindel.py [options]

Filter Indels from the output of pindel

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         make lots of noise
  -i SomeID.vcf, -inputVcf SomeID.vcf
                        Input vcf freebayes file which needs to be filtered
  -tsn SomeName, --tsampleName SomeName
                        Name of the tumor Sample
  -dp 0, --totaldepth 0
                        Tumor total depth threshold
  -ad 5, --alleledepth 5
                        Tumor allele depth threshold
  -tnr 5, --tnRatio 5   Tumor-Normal variant frequency ratio threshold
  -vf 0.01, --variantfrequency 0.01
                        Tumor variant frequency threshold
  -o /somepath/output, --outDir /somepath/output
                        Full Path to the output dir.
  -min 25, --min_var_len 25
                        Minimum length of the Indels
  -max 500, --max_var_len 500
                        Max length of the Indels
  -hvcf hostpot.vcf, --hotspotVcf hostpot.vcf
                        Input bgzip / tabix indexed hotspot vcf file to used
                        for filtering