User: User000

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User000370
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Posts by User000

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Imputation with BEAGLE 5.1 giving an inconsistent number of alleles error
... Hello, I did a variant calling of 200 genotypes with freebayes. I filtered for the DP and GQ values and the genotypes that did not pass the filter were set to `./.`. I now want to impute these filtered vcf files with BEAGLE v5.1. But it is giving me the following error: java.lang.IllegalArgume ...
freebayes beagle written 5 weeks ago by User000370 • updated 25 days ago by gabri.mochales10
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Comment: C: Freebayes variant calling understanding
... thank you Kevin, I still haven't found a solution for the second part of my question, but if you want to close the thread, go ahead. ...
written 11 weeks ago by User000370
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Answer: C: Extract several columns from a VCF file
... Yes, now I found a solution: bcftools view -S in.txt in.vcf > out.vcf If you were polite and just wrote your latest comment, we would have avoided upsetting each other. Don't take for granted that understanding some concepts are easy for everybody like they are for you. Sometimes we just ne ...
written 11 weeks ago by User000370
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Comment: C: Extract several columns from a VCF file
... I wouldn't be asking questions here if I wasn't stuck. So sorry I am not as brilliant as you are! Also, if you are not willing to help, just do not comment, as I am a grown up person and I know how to study! thanks ...
written 11 weeks ago by User000370
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Comment: C: Extract several columns from a VCF file
... vcf format #header1 #header2 #etc #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ID1 ID2 ID3 ID4 ID5...ID100 I need to get some of this ID's ...
written 11 weeks ago by User000370
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Comment: C: Extract several columns from a VCF file
... a bit more details would be much appreciated, as I studied it, but without any success. ...
written 11 weeks ago by User000370
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Extract several columns from a VCF file
... Hello, I have a vcf file with 100 genotypes. I want to extract information on 10 specific genotypes and I have a list of their ID's. Any ideas which tool could be used? ...
vcf written 11 weeks ago by User000370 • updated 11 weeks ago by omid.alavijeh40
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Freebayes adjusting parameters to "force" homozygous call
... How to change the freebayes parameters in following situations: Even if there is only one reference allele with a high mapping quality 60 freebayes would result in a 0/1 call. For me this could be an alternative allele. Any suggestions? [image here][1] [1]: https://ibb.co/album/hUsYAa ...
variant calling freebayes written 12 weeks ago by User000370 • updated 14 days ago by Biostar ♦♦ 20
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Comment: C: Freebayes variant calling understanding
... Ah I see, so you mean the allele is different from other genotypes! ...
written 12 weeks ago by User000370
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Comment: C: Freebayes variant calling understanding
... that sounds reasonable, but when I have a look at the loci in bam file, I can see only reference allele and alternative allele, something like this: [image here][1] [1]: https://ibb.co/album/duefqa ...
written 12 weeks ago by User000370

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