Could not find chromosome length for bam file

[ZheZhang-ZZ]

Hi Robbie,

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:

samtools view -H /disk201/zz/genotypingExplore/CleanFastq/04_CLEANBAM/35_AQ_CCTA.bam

@HD     VN:1.5  GO:none SO:coordinate
@SQ     SN:chr1 LN:274330532
@SQ     SN:chr10        LN:69359453
@SQ     SN:chr11        LN:79169978
@SQ     SN:chr12        LN:61602749
@SQ     SN:chr13        LN:208334590
@SQ     SN:chr14        LN:141755446
@SQ     SN:chr15        LN:140412725
@SQ     SN:chr16        LN:79944280
@SQ     SN:chr17        LN:63494081
@SQ     SN:chr18        LN:55982971

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

[ZheZhang-ZZ]

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.