sequences data QC
I want to do the QC process for sequence data. But can't not find the relative information. I have done the GWAS QC process like sex check, Genotyping call rate check, Homozygosity check, Cryptic relatedness check, Divergent ancestry check, Remove SNPs with low GCR or MAF and Remove SNPs violating HWE. It's same as sequences?? But I have found that sequences data have much missing call rate for snp.
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chengyi31000 •
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It's unclear which data (fastq? bam? vcf?) you have and which QC you want to perform. Please elaborate.
My data is VCF file. I am wondering what process need to do and what's the threshold of remove snp call rate, HWE...etc. Thank you!