hapcut2 linkfragments error

[jakobcmueller]

Dear Vikas Bansal,

I am using your software Hapcut2 to phase all genotypes of a given vcf (including 0/0 in order to distinguish 0/0 and ./.).

At the linkfragments.py step I had the following error message:

mueller@ux4012:/media/sdb/Blue_tit/HFC_10x$ python3 ~/bin/HapCUT2-master/utilities/LinkFragments.py --bam /raw_data_kemp/GENOMICS/Blue_tit/HFC_seq/P11159/analysis/J.Mueller_18_01_custom/01-longranger_customgenome/P11159_101_custom/outs/phased_possorted_bam.bam --VCF selvar_101.recode.vcf --fragments unlinkhapcut_101 --out linkhapcut_101
Linking 10X fragments on chromosome: chr1_part1
Traceback (most recent call last):
File "/home/mueller/bin/HapCUT2-master/utilities/LinkFragments.py", line 486, in
link_fragments(args.fragments,args.VCF,args.bam_file, args.outfile, args.distance, args.single_SNP_frags)
File "/home/mueller/bin/HapCUT2-master/utilities/LinkFragments.py", line 321, in link_fragments
flist = read_fragment_matrix(hairs_file,vcf_file,chrom_filter=curr_chrom)
File "/home/mueller/bin/HapCUT2-master/utilities/LinkFragments.py", line 252, in read_fragment_matrix
flist.sort(key=lambda x: x.seq[0][0])
File "/home/mueller/bin/HapCUT2-master/utilities/LinkFragments.py", line 252, in
flist.sort(key=lambda x: x.seq[0][0])
IndexError: list index out of range

The bam file comes from a 10XG LongRanger run and includes 500 scaffolds. The vcf file comes from GATK Haplotypecaller.

About which list is the error?

I hope you can help or advice me,
with best wishes,

Jakob