astrinaki_maria
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Latest activity by astrinaki_maria-
astrinaki_maria commented,
Hi Pamela, Thank you for your answer! yes it seems that we have Allele Fraction less than 0.5 , as you can see below 12 122945877 . CAAA C 47.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.319;DP=17;Exc...
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astrinaki_maria commented,
Hi Pamela, thank you for your quick response. So, in the below example 1 1922670 . A G 2843.95 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.302e+00;DP=55;ExcessHet=1.5490;FS=10.558;MQ=60.00;MQRankSum=0....
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astrinaki_maria commented,
Hi Pamela thank you very much for your reply, I run AlleleFraction annotation and I got the below record for the three samples 6 31896527 . G A 10481.73 PASS AC=6;AF=1.00;AN=6;DP=299;ExcessHet=3.0...
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astrinaki_maria commented,
Dear Pamela, thank you, I truly appreciate your help, I used the --MIN_AB parameter and it actually worked! However I still have some questions about homozygosity and heterozygosity. If I am not mi...
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astrinaki_maria commented,
Dear Pamela thank you so much for your reply! Could you advise me what would be the best way to calculate allele balance using this tool ? Thank you in advance, Maria
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astrinaki_maria created a post,
GATK4 VariantAnnotator doesn't support AlleleBalance
Hello, I try to analyze a trio sample (mother, father, son) so I used the following pipeline "Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode" then I did variant recal...
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astrinaki_maria commented,
Hello Wbsimey and Genevieve, I face the same problem, did you find the solution? Best regards, Astrinaki Maria