User: hdtms

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hdtms 20
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Posts by hdtms

<prev • 22 results • page 1 of 3 • next >
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Identify hits with Infernal
... I have wheat fasta file and I have to identify how many hits of MIR1122 pass the significance filter in a prediction with Infernal, but I have no idea how to do this. I have read the Infernal manual, and I know how to predict using just the wheat fasta but I can't do the filter. ...
infernal prediction written 10 months ago by hdtms 20
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Strange FST values
... I calculated the FST of my data using Plink and VCFtools they both gave strange values for the same positions, such as FST of 1 ; 116 ; -76. Any idea why I get this? ...
plink vcftools fst written 17 months ago by hdtms 20
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Comment: C: Annovar Annotation Dificulties
... Soory for answering so late. I do the convertion with the following command: convert2annovar.pl -format vcf4 Am01.vcf -outfile Am01.avinput And I don't get any .invalid_input files ...
written 20 months ago by hdtms 20
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Comment: C: Annovar Annotation Dificulties
... I do not know how I can see which calls were thrown out but what I get in the Log file is this: NOTICE: Done with 63481 transcripts (including 15216 without coding sequence annotation) for 27720 unique genes NOTICE: Processing next batch with 15922 unique variants in 15922 input lines WARNING: A to ...
written 21 months ago by hdtms 20
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Annovar Annotation Dificulties
... Hi I split my inicial Indel vcf by sample and then converted each Indel vcf into the Annovar input file , I got several sequences thrown out because of ORF errors. So my first doubt is about this is it because of the conversion of the files or errors already in my file. Next I filtered using the G ...
annotation indels written 21 months ago by hdtms 20 • updated 21 months ago by Biostar ♦♦ 20
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Comment: C: Indel Inbreeding Coefficient values vey different from SNPs
... Thank you for your response. They are di-allelic (SNPs and Indels). I will do a literature research to see what I can find. ...
written 22 months ago by hdtms 20
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Indel Inbreeding Coefficient values vey different from SNPs
... My Inbreeding Coefficient in Indels is very different from SNPs . I don't know if this is normal or if I can apply this to Indels. Any suggestions? ...
indels written 22 months ago by hdtms 20
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Annovar Region Annotation
... I used Annovar to annotate my Indel VCF file, I followed the manual steps and the Filter Annotation and Gene Annotation worked fine but I'm getting the Region Annotation. I tried changing the reference libraries and I still don't get any result, nor an error message. Any ideas? ...
annovar written 23 months ago by hdtms 20 • updated 18 months ago by Biostar ♦♦ 20
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Problem phasing Indels
... Hi I tried to phase my Indel vcf file using BEAGLE and I got an error, I then read in these forum that BEAGLE can't be used for Indels. My question is: Is there another program to do this? ...
indels phasing beagle written 2.0 years ago by hdtms 20
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Annovar warning message
... I'm using Annovar for variant annotation I want to input a vcf file and I get this warning message: #perl convert2annovar.pl Indel_Autoss.vcf -format vcf4 > Indel_Aut_Ann.vcf4 WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If ...
annovar warning written 2.0 years ago by hdtms 20 • updated 2.0 years ago by h.mon28k

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