Snp-pileup failed to return data

[boonhaohong]

Hi, I am using FACETS for CNV. However, when I try to use snp-pileup for my vcf, normal bam file and tumour bam file, it return only headers in my output file as shown below:
Chromosome,Position,Ref,Alt,File1R,File1A,File1E,File1D,File2R,File2A,File2E,File2D.

I ensure all the bam files are sorted and I have tried to strip the "chr" prefix for the bam file but failed too.

The vcf file I am using is dbsnp_153.hg38.vcf.

[boonhaohong]

It worked when I change my vcf to 00-common_all.vcf.gz

[graceooh]

@veseshan I have the same problem after using a vcf files from dbsnp. I have not tried it with another vcf file but why would it work with one and not another?

[veseshan]

The NCBI location https://ftp.ncbi.nlm.nih.gov/snp/organisms/ only lists builds 150 and 151. How are you getting the build 153 files? You may want to see how the files dbsnp_153.hg38.vcf and 00-common_all.vcf.gz differ.

[graceooh]

They are available on https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi . I'll try it with 150 instead and see if the older versions work. Thank you!

[graceooh]

When I tried it with build 155 it did not work but It works with build 150. I'll look into the difference. Thank you!

[veseshan]

Chromosomes are named NC_000001.10 etc in build 155 (probably from 152 on). That is likely the cause.

[bwubb]

Im not certain if this is the same issue as the OP. I get some results from snp-pileup, but I only get chromosomes 1-9 and X. Any two digit chromosome is missing. Im using GRCh38 reference and a dbSNP 156 vcf.

[baoyl818]

Im not certain if this is the same issue as the OP. I get some results from snp-pileup, but I only get chromosomes 1-9 and X. Any two digit chromosome is missing. Im using GRCh38 reference and a dbSNP 156 vcf.

我也遇到这个问题了，请问你现在解决了吗？
我后来使用 cnv_facets.R 了，就没有这个问题了。