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how to convert whole genome sequencing datasets to use for GWAS

I have processed the plant whole genome sequencing datasets and extracted the below data from combined vcf file; could anyone please help me now how to convert this dataset to use for GWAS analysis using the GAPIT tool.

CHROM   POS ID  REF ALT QUAL    FILTER  Abermagic   BarM    Bowie   Cal Cont    Cross   Durendal    Glasker Ivana   Swan
NC_009950.1 63326   .   T   G   113.86  PASS    0/0 0/0 0/0 0/0 0|1 ./. 0/0 0/0 0/0 ./.
NC_009950.1 63334   .   C   T   113.86  PASS    0/0 0/0 0/0 0/0 0|1 ./. 0/0 0/0 0/0 ./.
NC_009950.1 66285   .   C   T   44.31   PASS    0/0 0/0 ./. 0|1 0/0 0/0 0/0 0/0 0/0 ./.
NC_009950.1 66310   .   T   A   40.81   PASS    0/0 0/0 ./. 0|1 0/0 0/0 0/0 0/0 0/0 0/0

I have added the SNPs filterling pipeline here;

# Step 1: Extract SNPs
gatk SelectVariants \
  -R ${REFERENCE} \
  -V ${INPUT_VCF} \
  --select-type-to-include SNP \
  -O ${SNP_VCF}

# Step 2: Apply your SNP filters
gatk VariantFiltration \
  -R ${REFERENCE} \
  -V ${SNP_VCF} \
  -O ${FILTERED_SNP_VCF} \
  --filter-name "QD2" --filter-expression "QD < 2.0" \
  --filter-name "QUAL30" --filter-expression "QUAL < 30.0" \
  --filter-name "SOR3" --filter-expression "SOR > 3.0" \
  --filter-name "FS60" --filter-expression "FS > 60.0" \
  --filter-name "MQ40" --filter-expression "MQ < 40.0" \
  --filter-name "MQRankSum-12.5" --filter-expression "MQRankSum < -12.5" \
  --filter-name "ReadPosRankSum-8" --filter-expression "ReadPosRankSum < -8.0"

# Optional Step 3: Keep only PASS SNPs
gatk SelectVariants \
  -R ${REFERENCE} \
  -V ${FILTERED_SNP_VCF} \
  --exclude-filtered true \
  -O ${PASS_SNP_VCF}
gwas gapit r
• 270 views • link
written by ngseq • ngseq

How have you 'extracted' the below data? More information would help

A simple pipeline might look like: filtering for only biallelic variants (maybe already done), filtering out variants that are rare in the pop/missing from many samples (maybe already done). Both steps in plink. Then use plink to generate to a genotype table using the --recodeA option. GAPIT should be able to use that alongside your phenotyping table (assuming you have it)

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written by samuel.a.odonnell samuel.a.odonnell

thank you so much @Samuel, I have added a SNPs filtering pipeline above. I would like to extract INDEL same way and then will do hard filtering and then would like to combine both SNPs and INDEL for extracting targeted genes INDEL and SNPs to link with gene expression. Is there any tool that help extract the target genes SNPs and INDEL. This is completely different experiment from GWAS but still using the same dataset.

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written by ngseq • ngseq

how would it be different from the workflow above aside

 --select-type-to-include INDEL

and the other parameters specific to INDEL ?

?

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for all help. I was able to extract the SNPs and INDELs and then also concatenate after using the hard filtering for SNPs and INDELs. Could you please help now how to extract targated genes SNPs and INDELs using the GTF annotation file. Thanks again for all help.

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written by ngseq • ngseq

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