SNP calling exercise answers part 2: Revision history

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8 January 2025

  • curprev 13:2613:26, 8 January 2025‎ Gabre talk contribs‎ 1,960 bytes +1,960‎ Created page with " '''Q1''' First running: <pre> gatk VariantFiltration -V NA24694.vcf.gz -O NA24694_hf.vcf.gz -filter "DP < 10.0" --filter-name "DP" -filter "QUAL < 30.0" --filter-name "QUAL30" -filter "SOR > 3.0" --filter-name "SOR3" -filter "FS > 60.0" --filter-name "FS60" -filter "MQ < 40.0" --filter-name "MQ40" </pre> and <pre> bcftools view -H NA24694_hf.vcf.gz |grep -v PASS |wc -l </pre> Gives us 4005 sites. <pre> bcftools view -H --type=..."
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