User: Jamie Watson

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Posts by Jamie Watson

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Downloading CADD scores
... Thank you. I was using wrong HTTP links. ...
written 25 days ago by Jamie Watson0
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difference in the content of a tsv and bigwig file
... I have downloaded both the tsv file and bigwig file for CADD scores. However, upon inspection these two files contain different information. For example a tsv file has following content: #Chrom Pos Ref Alt RawScore PHRED 1 10001 T A 0.702541 8.478 1 10001 T C 0.750954 8.921 1 ...
bigwig written 26 days ago by Jamie Watson0
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Downloading CADD scores
... I want to download CADD scores (**All possible SNVs of GRCh38/hg38**) from the following webpage: [https://cadd.gs.washington.edu/download][1] However for each download link it says **US | DE**. I can't find an explanation for what these two things mean. Can someone explain what it means or point ...
snp cadd written 5 weeks ago by Jamie Watson0 • updated 5 weeks ago by Pierre Lindenbaum133k
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Lifting over from Hg37 to Hg38 coordinates doesn't work
... I downloaded these csv files from the following link: [https://human.genome.dating/download/index][1] These csv files are comma delimited but have white spaces as well. That is each comma is followed by a white space. So I read each file using pandas and remove the white spaces using the following ...
genome liftover written 7 weeks ago by Jamie Watson0 • updated 7 weeks ago by Qiongyi100
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Comment: C: convert .csv file to a .vcf file
... So the error says that a key is missing. And that key apparently is a white space but INFO column does not have any blank spaces. I am not sure what is wrong with awk script. ...
written 7 weeks ago by Jamie Watson0
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Comment: C: convert .csv file to a .vcf file
... The script still doesn't work. It gives the following error: **Exception in thread "main" java.lang.IllegalStateException: Key found in VariantContext field INFO at 1:10539 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.** And looking at ...
written 7 weeks ago by Jamie Watson0
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Comment: C: convert .csv file to a .vcf file
... Yes I didn't add that. I'll try again with tr -d ' '. Thanks. ...
written 7 weeks ago by Jamie Watson0
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Comment: C: convert .csv file to a .vcf file
... Hi again, Yes I made it work. However, when I try to liftOver using GATK Picard, it says **'The provided VCF file is malformed at approximately line number 26: 10539 is not a valid start position in the VCF format, for input source'**. Could you explain why I am getting this error? I have used the ...
written 7 weeks ago by Jamie Watson0
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Comment: C: convert .csv file to a .vcf file
... I ran the command but it gives me the following error: gzip: stdin: unexpected end of file ...
written 7 weeks ago by Jamie Watson0
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convert .csv file to a .vcf file
... I have csv files from the following link: https://human.genome.dating/download/index However, they use hg37 human coordinates and I am using hg38. So I need someway to lift over these csv files to h38 coordinates. I was thinking of converting these csv files to vcf files and then use Picard tool t ...
genome snp written 8 weeks ago by Jamie Watson0 • updated 8 weeks ago by Pierre Lindenbaum133k

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