gravatar for Jamie Watson

2 hours ago by

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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