bmvdgeijn
commented
4 years ago Hi Saideep,
I believe this means there is a mismatch between the SNP and genotype files and the bed-like file. Is there a SNP on chr1:74570 in your input genotypes? Another possibility is there is an off by one and your SNP file is 0-based and bed is 1-based.
On Sat, Nov 9, 2019 at 8:15 PM Saideep Gona notifications@github.com<mailto:notifications@github.com> wrote:
In the: extract_haplotype_read_counts.py step, I keep getting errors such as the following:
WARNING: could not find test SNP at position 1:74570
I'm having trouble tracing the issue back to the source as it is complicated to follow. Do you know the likely causes of this? I'm pretty sure I made the bed-like file to specification.
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In the: extract_haplotype_read_counts.py step, I keep getting errors such as the following:
WARNING: could not find test SNP at position 1:74570
I'm having trouble tracing the issue back to the source as it is complicated to follow. Do you know the likely causes of this? I'm pretty sure I made the bed-like file to specification.