I'd like to consult an error raised when I tried to impute extemely low coverage WGS samples (<0.03×):
Error in quilt_get_chromosome_length(iBam = 1, bam_files = bam_files, :
Could not find chromosome length for file:/disk201/zz/genotypingExplore/CleanFastq/04_CLEANBAM/35_AQ_CCTA.bam
But the chromosome name (chr1) used in QUILT matches the header of the bam file, as follows:
The weird thing is that no such "chromosome length" error was reported when I changed to use another haplotype reference panel with smaller sample size.
Sorry, the issue raised because the HRP was prepared by QUILT_prepare_reference with wrong chromosome name. After I changed the chromosome name, the probleme was solved.
Hi Robbie,
I'd like to consult an error raised when I tried to impute extemely low coverage WGS samples (<0.03×):
But the chromosome name (
chr1
) used in QUILT matches the header of the bam file, as follows:The weird thing is that no such "chromosome length" error was reported when I changed to use another haplotype reference panel with smaller sample size.
Could you please help me out?
Best, Zhe