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, 16:24, 15 June 2014
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| Use tabix to extract that from the VCFs: | | Use tabix to extract that from the VCFs: |
| ${GC}/bin/tabix ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz 22:36907000-36907100 |less -S | | ${GC}/bin/tabix ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz 22:36907000-36907100 |less -S |
| + | |
| + | Remember, type 'q' to quit less. |
| + | q |
| | | |
| ;Are there any variants in this region? | | ;Are there any variants in this region? |
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| zcat ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz |grep "#CHROM" | | zcat ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz |grep "#CHROM" |
| * That will help you figure out it's genotype. | | * That will help you figure out it's genotype. |
| + | * Rerun the tabix command and scroll to find HG00551's genotype: |
| + | ${GC}/bin/tabix ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz 22:36907000-36907100 |less -S |
| + | |
| <ul> | | <ul> |
| <div class="mw-collapsible mw-collapsed" style="width:500px"> | | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
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| </div> | | </div> |
| </ul> | | </ul> |
| + | |
| + | Remember, type 'q' to quit less. |
| + | q |