Create SnpSift_exercise_KEY.md

lessons/SnpSift_exercise_KEY.md

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+---
+title: "SnpSift Exercises"
+author: "Will Gammerdinger, Meeta Mistry"
+date: "May 27, 2024"
+---
+
+In this exercise we will use the VCF file that we have generated  in order to practice parsing our apart our VCF. The VCF file is availible for download [here]().
+
+# Exercises
+
+**1)** Extract all of the stop codon losses
+
+```
+java -jar $SNPEFF/SnpSift.jar filter   "( ANN[*].EFFECT has 'stop_lost' ) " mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf 
+```
+
+**2)** Extract all of the SNPs on Chromosome 2 between 8Mb and 10.2Mb.
+
+```
+java -jar $SNPEFF/SnpSift.jar filter   "( CHROM = '2' ) & ( POS > '8000000' ) & ( POS < '10200000' ) " mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf
+```
+
+**3)** Extract all of the mutations that alter a splice site on Chromosome 11.
+
+```
+java -jar $SNPEFF/SnpSift.jar filter   "( CHROM = 'X' ) & ( ( ANN[*].EFFECT has 'splice_donor_variant' ) | ( ANN[*].EFFECT has 'splice_acceptor_variant' ) )" mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf
+```
+
+**4)** Extract all of the high impact mutations on Chromosome 12 or moderate impact mutations on Chromosome 3.
+
+```
+java -jar $SNPEFF/SnpSift.jar filter   "( ( CHROM = '12')  &  ( ANN[*].IMPACT has 'HIGH' ) ) | ( ( CHROM = '13') & ( ANN[*].IMPACT has 'MODERATE' ) )" mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf
+```
+
+[Next Lesson >>](11_IGV.md)
+
+[Back to Schedule](../schedule/README.md)
+
+
+***
+
+*This lesson has been developed by members of the teaching team at the [Harvard Chan Bioinformatics Core (HBC)](http://bioinformatics.sph.harvard.edu/). These are open access materials distributed under the terms of the [Creative Commons Attribution license](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.*