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 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.
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Jamie Watson •
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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.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.
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.