Merge different alignments of a read to improve phasing integrity and adjust parameter weights to enhance phasing accuracy. Allow the use of phased modification VCF to increase the proportion of tagged reads. Address some known issues.
phase (-t 24)
v1.6 SW
v1.6 #Block
v1.6 Block N50
v1.7 SW
v1.7 #Block
v1.7 Block N50
HG002 ONT R10.4.1 10x
1,137
7,212
774,928
1,117
7,100
807,877
HG002 ONT R10.4.1 20x
1,225
4,257
1,560,226
1,218
4,132
1,654,808
HG002 ONT R10.4.1 30x
1,194
3,499
1,903,900
1,180
3,372
2,042,500
HG002 ONT R10.4.1 40x
1,211
3,045
2,177,620
1,200
2,915
2,332,195
HG002 ONT R10.4.1 50x
1,216
2,797
2,470,461
1,213
2,679
2,606,645
HG002 ONT R10.4.1 60x
1,197
2,627
2,587,166
1,195
2,513
2,830,210
SW: Switch Error
Changes
60
59
58
57
fix the order of SNP, SV, and methylations
fix the lack of SV and methylations when SNP SV, and modification co-phasing
fix repeat position of SV and methylation
55
Merging different alignments of a read into a single alignment to enhance phasing integrity.
Correct the conditions for judging the VCF header.
52
Add two parameters baseQuality and edgeWeight guide to the --help list. Users can now decide what baseQuality threshold and edgeWeight they want to use.
49
The variants used in multiple VCFs will be accessed and stored in their respective chrVariant, even if multiple variants occur at the same coordinate, only one chrVariant from one VCF will be recorded.
48
When utilizing haplotag for read haplotype tagging, it will automatically detect whether the phased SNP file includes phased indels.
When performing read haplotype tagging with haplotag, it can use the --mod-file option to input the phased modification VCF.
Correcting the condition in ParsingBam.cpp for determining when a deletion variant that fall within the read's deletion cigar.
Summary
Merge different alignments of a read to improve phasing integrity and adjust parameter weights to enhance phasing accuracy. Allow the use of phased modification VCF to increase the proportion of tagged reads. Address some known issues.
SW: Switch Error
Changes
60
59
58
57
55
52
baseQualityandedgeWeightguide to the --help list. Users can now decide whatbaseQualitythreshold andedgeWeightthey want to use.49
chrVariant, even if multiple variants occur at the same coordinate, only onechrVariantfrom one VCF will be recorded.48
haplotagfor read haplotype tagging, it will automatically detect whether the phased SNP file includes phased indels.haplotag, it can use the--mod-fileoption to input the phased modification VCF.