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