Critical criteria for filtering variants by VariantFiltration

Question

[Alireza]

Hi all.

I run the GATK VariantFiltration with the following parameters (according to GATK recommendation) to find robust variants. Then I used them as input for annotating variants.

Do you have any suggestions for better filtration?

Is it recommended to run VariantFiltration on different variants (somatic, germline, CNV)?

For SNP:

gatk VariantFiltration \
        -R genome.fa \
        -V germline_raw_SNP.vcf \
        -O germline_filtered_SNP.vcf \
            -filter-name "QD_filter" -filter "QD < 2.0" \
        -filter-name "FS_filter" -filter "FS > 60.0" \
        -filter-name "MQ_filter" -filter "MQ < 40.0" \
        -filter-name "SOR_filter" -filter "SOR > 4.0" \
        -filter-name "MQRankSum_filter" -filter "MQRankSum < -12.5" \
        -filter-name "ReadPosRankSum_filter" -filter "ReadPosRankSum < -8.0" \
        -genotype-filter-expression "DP < 10" \
        -genotype-filter-name "DP_filter" \
        -genotype-filter-expression "GQ < 10" \
        -genotype-filter-name "GQ_filter"

For INDELS:

gatk VariantFiltration \
        -R genome.fa \
        -V germline_raw_INDEL.vcf \
        -O germline_filtered_INDEL.vcf \
            -filter-name "QD_filter" -filter "QD < 2.0" \
        -filter-name "FS_filter" -filter "FS > 200.0" \
        -filter-name "SOR_filter" -filter "SOR > 10.0" \
        -genotype-filter-expression "DP < 10" \
        -genotype-filter-name "DP_filter" \
        -genotype-filter-expression "GQ < 10" \
        -genotype-filter-name "GQ_filter"