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Recent Replies
Comment: Michigan Imputation Server does not impute all input files
by
WouterDeCoster
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Probably related to the warning on the chunks that were removed because of low reference overlap. Is the reference genome (hg19) correct?
Comment: gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.site
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Edmond
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These files are for hg38, not hg19.
Do you know were are the files for hg19 ?
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zack.saud
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Hi,
This answer is more than I hoped for... thank you for the info, I really appreciate it.
Best
Answer: Michigan imputation server input preparation
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vtran
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You can look at the QC_report after imputation to see which SNPs got excluded and why. Usually, a lot of SNPs are excluded because they are…
Answer: Sliding window plot using Python
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A_Lh
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This is a Python solution:
import pandas as pd
import numpy as np
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Comment: Miropeats download issue
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GenoMax
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You could give `mauve` ([LINK][1]) a try for start.
Plot type you show above are referred to as alluvial plots. You will need to find a wa…
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aritra90
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Found the solution for anyone interested.
The issue was in the reference file Chromosome IDs being "chr20" instead of "20" (as in the tar…
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gperez8
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Hello,
[Geneid Genes][1] (geneid.txt.gz) is an older transcript predictor algorithm that is based on the genome sequence alone and only …
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gokberk
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Fasta of a region from hg38, I was planning to self-align it and look for duplications etc. Then I will crop out the corresponding region f…
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GenoMax
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Align to the genome and then use the lists of captured regions that came with your kit/design to check on efficiency/coverage.
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gokberk
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It is indeed very old, but I guess most of such sequence alignment tools were developed in '90s, right? I want to have a look at the overal…
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Can you try `samtools view` to do the conversions of CRAM to BAM? Using a third party tool like Picard may not be following the latest CRAM…
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Hamid Ghaedi
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Please paste your code here and let other people see what you have tried. So they might be able to help with issue.
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