Question: difference in the content of a tsv and bigwig file
0
gravatar for Jamie Watson
8 weeks ago by
Jamie Watson0 wrote:

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     10001  T  G   0.719549    8.634
1     10002  A  C   0.713993    8.583

So for each position there is an alternate variant and for each alternate variant there is a CADD score.

However, I read bigwig file using python library bigwig and when I use intervals to get the correspond CADD score, I get only one score instead of three like in tsv

bw = pyBigWig.open("CADD_GRCh38-v1.6.bw")
bw.intervals('chr1',10001,10002)

The result I get is the following:

((10001, 10002, 8.854000091552734),)

Which variant does this score belong to? And how can I get a score for each of the alternate variant using bigWigFile.

bigwig • 189 views
ADD COMMENTlink written 8 weeks ago by Jamie Watson0
1

Your question is about CADD. Why is the only tag on your post the file format? That is not specific and will not get any attention from anyone looking at /t/cadd posts.

ADD REPLYlink written 8 weeks ago by Ram32k
1

Bigwig files are not allele-specific, they simply store one value for the nucleotide interval. You would need to read the documentation or see the code that generated the bigwig to see what exactly that value is related to this tsv file.

ADD REPLYlink written 8 weeks ago by ATpoint45k

Your previous questions have responses but no feedback on those responses. It is bad etiquette to "dine and dash" - that is, ask a question, get an answer because someone invested effort in your problem, and then leave wiithout so much as an acknowledgement, let alone giving back to the community.

ADD REPLYlink written 8 weeks ago by Ram32k
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