The problem occurs when I use SHAPEIT, the problem is as follows
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6 days ago

My code is as follows,At the end it has an error and I don't know how to fix it : shapeit \ -M genetic_map_hg38_withX.txt \ --input-bed chr22.bed chr22.bim chr22.fam \ --input-ref RefPanel.hap.gz RefPanel.legend.gz sample.txt \ --exclude-snp chr22.alignments.snp.strand.exclude\ -O chr22.phased

Segmented HAPlotype Estimation & Imputation Tool

MODE -phase : PHASING GENOTYPE DATA

  • Autosome (chr1 ... chr22)
  • Window-based model (SHAPEIT v2)
  • Reference panel of haplotypes used
  • MCMC iteration

Parameters :

  • Seed : 1659518618
  • Parallelisation: 1 threads
  • Ref allele is NOT aligned on the reference genome
  • MCMC: 35 iterations [7 B + 1 runs of 8 P + 20 M]
  • Model: 100 states per window [100 H + 0 PM + 0 R + 0 COV ] / Windows of ~2.0 Mb / Ne = 15000

Reading SNPs to exclude from input file in [chr22.alignments.snp.strand.exclude]

  • 277 snps found in the exclude list

Reading site list in [chr22.bim]

  • 9486 sites included
  • 277 sites excluded

Reading sample list in [chr22.fam]

  • 306 samples included
  • 306 unrelateds / 0 duos / 0 trios in 306 different families

Reading genotypes in [chr22.bed]

  • Plink binary file SNP-major mode

Reading sample list [/gpfs/lab/liangmeng/members/dongxinyu/SHAPEIT/sample.txt]

  • 5094 reference haplotypes included

Reading SNPs in [/gpfs/lab/liangmeng/members/dongxinyu/SHAPEIT/RefPanel.legend.gz]

  • 9486 reference panel sites included
  • 1049593 reference panel sites excluded

Reading reference haplotypes in [/gpfs/lab/liangmeng/members/dongxinyu/SHAPEIT/RefPanel.hap.gz]

ERROR: Line=9799 found=5096 fields, expected=5094

SHAPEIE ERROR • 199 views
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Your reference file seems to be truncated somehow but it's impossible to know how unless we can see those lines of a file. Is there any reason you are using a piece of software that is many versions out of date? You should strongly consider using a more recent version here. It'll also mean you won't have to work with antiquated file formats like .hap.

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Your mean is that the version of SHAPEIT2 is too old ?

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It's very old compared to the new version - shapeit4 is much, much faster (saving lots of energy in the process!) and more accurate and uses more standard file formats (vcf). I'm not related to shapeit at all, I just like to encourage people to use the most up to date software where they can. shapeit2 won't give you 'bad' results though.

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