SHAPEIT4 output for haptag

[Yijun-Tian]

Hi, To further improve the read level phasing performance, we use the population based (genotype based) haplotype reference to adjusting the longphase phase vcf in SHAPEIT4. Here is the output VCF.

##  longphase phase VCF
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample
chr22   10522327        chr22_10522327_T_C      T       C       16      PASS    .       GT:GQ:DP:AD:VAF:C:PS    1/1:4:5:5:1:DV:.
chr22   10522392        chr22_10522392_C_T      C       T       16      PASS    .       GT:GQ:DP:AD:VAF:C:PS    1/1:4:5:5:1:DV:.
chr22   10522452        chr22_10522452_C_T      C       T       18.8    PASS    .       GT:GQ:DP:AD:VAF:C:PS    1/1:6:5:5:1:DV:.

##  SHAPEIT4 output VCF
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample
chr22   10526217        chr22_10526217_A_G      A       G       .       .       AC=2;AF=1;CM=0  GT      1|1
chr22   10526550        chr22_10526550_G_A      G       A       .       .       AC=2;AF=1;CM=0.000681428        GT      1|1
chr22   10572965        chr22_10572965_A_C      A       C       .       .       AC=2;AF=1;CM=0.0956619  GT      1|1
chr22   10573343        chr22_10573343_C_G      C       G       .       .       AC=2;AF=1;CM=0.0964354  GT      1|1

However, when I use the VCF from SHAPEIT4 for haplotagging, error happens like below:

$  ~/longphase haplotag -s Shannon/shapeit4/s246.chr22.snv.vcf.gz -b s246.sorted.bam -r hg38.alignmt.fa -o s246.chr22
phased SNP file:   Shannon/shapeit4/s246.chr22.snv.vcf.gz
phased SV file:
input bam file:    s246.sorted.bam
input ref file:    hg38.alignmt.fa
output bam file:   s246.chr22.bam
number of threads: 1
write log file:    false
log file:
-------------------------------------------
filter mapping quality below:  20
percentage threshold:          0.6
tag supplementary:             false
-------------------------------------------
parsing SNP VCF ... terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoi
Aborted (core dumped)

Since the SHAPEIT4 output only 1 phase set ideally, could you clarify what INFO/FORMAT fields are needed for the haplotag step? I was thinking to define these field by myself so that can use haplotag to label each read for downstream analysis.

Thanks,

[twolinin]

Hi, @Yijun-Tian

I performed some tests and did not encounter this error message. Could you please provide the version of LongPhase you are using, and the SHAPEIT4 VCF header you used?

Thanks

[Yijun-Tian]

Thanks @twolinin ! I am using longphase 1.5.1 for the haplotagging:

shapeit4]$ longphase --version
Version: 1.5.1
Usage: main <command> [options]
               phase      run phasing algorithm.
               haplotag   tag reads by haplotype.
               modcall    convert bam file to modification vcf file.

Here is the header of SHAPEIT4 VCF:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=16/08/2024 - 15:36:24
##source=shapeit4.1.3
##contig=<ID=chr22>
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count">
##INFO=<ID=CM,Number=A,Type=Float,Description="Interpolated cM position">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased genotypes">
##bcftools_viewVersion=1.17+htslib-1.17
##bcftools_viewCommand=view -h s246.chr22.snv.vcf.gz; Date=Fri Aug 23 09:13:21 2024
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample

[twolinin]

Hi @Yijun-Tian

Please modify your header before ##contig=<ID=chr22> after ##contig=<ID=chr22,length=242193529>

Thanks

[Yijun-Tian]

Thanks, @twolinin. Haptag now works with the modification you noted.