whatshap --version
1.7

whatshap phase --ignore-read-groups --indels \
-r GCA_000001405.15_GRCh38_no_alt_analysis_set.fa \
hg002.wf_snp.vcf.gz \
hg002.sup.60x.bam \
-o whatshap_hg02_60x.vcf

bgzip -c whatshap_hg02_60x.vcf > whatshap_hg02_60x.vcf.gz
tabix -p vcf whatshap_hg02_60x.vcf.gz

whatshap haplotag --ignore-read-groups  \
whatshap_hg02_60x.vcf.gz hg002.sup.60x.bam \
-r GCA_000001405.15_GRCh38_no_alt_analysis_set.fa \
-o hg002.sup.60x.whatshap.haplotag.bam

samtools index -@ 24 hg002.sup.60x.whatshap.haplotag.bam

whatshap stats --gtf whatshap_hg02_60x.gtf whatshap_hg02_60x.vcf.gz

~/methphaser/meth_phaser_parallel \
-b hg002.sup.60x.whatshap.haplotag.bam \
-r GCA_000001405.15_GRCh38_no_alt_analysis_set.fa \
-g whatshap_hg02_60x.gtf \
-vc whatshap_hg02_60x.vcf.gz  \
-o work

[E::bam_parse_basemod] MM tag refers to bases beyond sequence length
Traceback (most recent call last):
  File "/home/jyunhong104/methphaser/methphasing", line 1471, in <module>
    main(sys.argv[1:])
  File "/home/jyunhong104/methphaser/methphasing", line 1437, in main
    ) = get_assignment_max(
  File "/home/jyunhong104/methphaser/methphasing", line 898, in get_assignment_max
    base_modification_list = get_base_modification_dictionary(  # build the dictionary with snp phased reads
  File "/home/jyunhong104/methphaser/methphasing", line 239, in get_base_modification_dictionary
    if methylation_identifier_0 in list(mm.keys()):
AttributeError: 'NoneType' object has no attribute 'keys'
[W::bam_next_basemod] MM tag refers to bases beyond sequence length
Traceback (most recent call last):
  File "/home/jyunhong104/methphaser/methphasing", line 1471, in <module>
    main(sys.argv[1:])
  File "/home/jyunhong104/methphaser/methphasing", line 1437, in main
    ) = get_assignment_max(
  File "/home/jyunhong104/methphaser/methphasing", line 898, in get_assignment_max
    base_modification_list = get_base_modification_dictionary(  # build the dictionary with snp phased reads
  File "/home/jyunhong104/methphaser/methphasing", line 239, in get_base_modification_dictionary
    if methylation_identifier_0 in list(mm.keys()):
AttributeError: 'NoneType' object has no attribute 'keys'
[W::bam_next_basemod] MM tag refers to bases beyond sequence length
Traceback (most recent call last):
  File "/home/jyunhong104/methphaser/methphasing", line 1471, in <module>
    main(sys.argv[1:])
  File "/home/jyunhong104/methphaser/methphasing", line 1437, in main
    ) = get_assignment_max(
  File "/home/jyunhong104/methphaser/methphasing", line 898, in get_assignment_max
    base_modification_list = get_base_modification_dictionary(  # build the dictionary with snp phased reads
  File "/home/jyunhong104/methphaser/methphasing", line 239, in get_base_modification_dictionary
    if methylation_identifier_0 in list(mm.keys()):
AttributeError: 'NoneType' object has no attribute 'keys'

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