ShapeIT check problematic SNPs

0

Hello All,

I am using shapeit to phase my genotype data using 1000G phase3 as a reference genome. In order to phase my genotypes, I am using SHAPEIT.
in the first step, I am using the command shapeIT to remove the problematic SNPs as has been mentioned in the link below:
Phasing with SHAPEIT

However, when in ran the second round of SHAPEIT -check to exclude the problematic variants using --exclude-snp Prephased/MyData_chr"${chr}"_alignments.snp.strand.exclude (the link above), I still get error and files with alignment.snp.strand.exclude.

So here are my questions:

  • Is it correct not to get all the problematic SNPs/variants in the first round of shapeit --check?
  • Should I continue this step (below) again to remove the newly found problematic SNPs/variants until I get no error?

Thank you for your responses,

for chr in X {1..22}; do 

  plink --bfile MyData --chr "${chr}" --make-bed --out temp

  if [ "${chr}" != "X" ]

  then

    srun --mem=8 --cpus-per-task=4 --partition=serial 

      shapeit 

        -check 

        -B temp 

        -M library/1000GP_Phase3/genetic_map_chr"${chr}"_combined_b37.txt 

        --input-ref library/1000GP_Phase3/1000GP_Phase3_chr"${chr}".hap.gz library/1000GP_Phase3/1000GP_Phase3_chr"${chr}".legend.gz library/1000GP_Phase3/1000GP_Phase3.sample 

        --exclude-snp Prephased/MyData_chr"${chr}"_alignments.snp.strand.exclude 
        -T 8 ;
  fi

done ;

rm temp.* ;


genotypes


imputev2


shapeit


problematic

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