why is there "." in Filter?
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22 months ago
arshiya.g02 ▴ 10

This was the command I used sudo ./gatk HaplotypeCaller -R /home/arshiya/efs/FastQC/hg38.fa -I /home/arshiya/efs/FastQC/sample_sort_reads.bam -O /home/arshiya/efs/FastQC/sample_haplo.vcf.gz and the following was the output I got

chr1    7820343 .   A   AATCCATGAAATGGCATACGATCAACTAATGTGACTGTATAATCTTGTGGTAAAGAAGTAGT  121.84  .   AC=2    AF=1.00 AN=2    DP=3    ExcessHet=3.0103    FS=0.000    MLEAC=1 MLEAF=0.500 MQ=48.00    QD=25.36    SOR=2.833   GT:AD:DP:GQ:PL  1/1:0   3:3:9:135   9   0
chr1    11979551    .   TGA T   78.28   .   AC=2    AF=1.00 AN=2    DP=2    ExcessHet=3.0103    FS=0.000    MLEAC=1 MLEAF=0.500 MQ=40.00    QD=28.73    SOR=2.303   GT:AD:DP:GQ:PL  1/1:0   2:2:6:90    6   0
chr1    11979558    .   G   GCCTCCACAAATTGTTAATCCCGGCATACCATCTTCAATCGCTTC   78.32   .   AC=2    AF=1.00 AN=2    DP=2    ExcessHet=3.0103    FS=0.000    MLEAC=1 MLEAF=0.500 MQ=40.00    QD=30.97    SOR=2.303   GT:AD:DP:GQ:PL  1/1:0   2:2:6:90    6   0
next-gen • 456 views
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22 months ago
benformatics ★ 2.1k

You need to apply a filter...?

Did you read the GATK manual and follow the best practices?

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yes I went through the manual and how to apply filter?

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