Extracting methylation haplotypes from sequence alignment files

[meb326]

Hi dinhdiep,

I'm very interested in your work and want to conduct methylation haplotype analysis on my bisulfite sequencing data. I am having trouble generating CpG haplotype files using your code. When I try the test example:
./scripts/bam2cghap.sh allcpg/cpg.small.txt.gz BAMfiles/Colon_primary_tumor_sept9_promoter.bam test

I get this error for many lines:
Use of uninitialized value $ref_seq in concatenation (.) or string at bin/getHaplo_PE_cgOnly.pl line 161, line 28.

Could you help me to get this to work? I would really appreciate it.

[long692108]

I am also interested in this work. Did you have solve this problem?

[kythol]

I have the same error