Vincent Appiah
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Activity overview
Latest activity by Vincent Appiah-
Vincent Appiah commented,
Genevieve Brandt (she/her) In my info fields I have F1R2 and F2R1. Is this expected or only one of them is supposed to be there.? PS. The samples were sequenced in two lanes. So I merged them b...
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Vincent Appiah commented,
Is this for gerline only or it applies to somatic variants as well.
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Vincent Appiah commented,
Genevieve Brandt (she/her). Can you help clarify this question? Thanks
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Vincent Appiah commented,
Genevieve Brandt (she/her) I resolved the issue. Looking the GATK best practises , I realised my command was not working because I had less than 10 samples. I had to remove the -an InbreedingCoeff...
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Vincent Appiah commented,
Genevieve Brandt (she/her). I guess I have to annotated with Mills_100G_standard_indels file. Vincent
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Vincent Appiah commented,
Hi Pamela Bretscher I have a similar problem. In my case, running VariantRecalibrator in SNP mode works but INDEL mode gives the error message given by chenglei Please advice.
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Vincent Appiah commented,
Thanks for the clarification Priyadarshini Thirunavukkarasu. What I like to know is when doing joint variant calling, does gatk look for only variants that are common to all the samples?
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Vincent Appiah commented,
OK. Thanks Buts its a bit confusing. When I run GenotypeGVCFs on the individual vcfs generated using the HaplotypeCaller, the number of variants were different for each sample. Sample No. of ...
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Vincent Appiah commented,
Priyadarshini Thirunavukkarasu I am showing results for just three samples but its the same for the others I tried with one position and are the output COUNTS OF SNPS AND INDELS sample indels ...
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Vincent Appiah commented,
Here is an example. I used bcftools to count the number of variants identified samples=(100N 100T 10T)for sample in ${samples[@]};do echo $sample $(bcftools view -s $sample $vcf|grep -v -c '^#');...