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03_​Variant_​Calling_​(Linux_​or_​Mac)_​solution

(THIS EXCERCISE WONT WORK ON WINDOWS OS, AS SAMTOOLS IS NOT AVAILABLE ON WINDOWS)Exercise 3: Variant Calling 1. Configure the Input File node labled (BAM alignment file) by selecting the BAM file human_hbb_gene.bam located under the provided data folder. 2. Similarly, configure the Input File node labled (Reference gene) by selecting the FASTA file human_hbb_gene.fasta located under the provided data folder. 3. Use the provided SortBAM node to sort the results. The result has to be sorted before variant calling. 4. Perform variant calling using SamtoolsMPileup node. (Hint: Connect the original Reference Genome to the optional port.) 5. The result from the previous step is a binary file in BCF format. Use BcfToVcf node to convert it to a human readable (VCF) format persist files by moving them from tmplocations to a directory of choice Variant CallerConverterSort BAMRead BAM alignment fileReference gene SamtoolsMPileup BcfToVcf SortBam Input File Input File Copy/Move Files Port to URI (THIS EXCERCISE WONT WORK ON WINDOWS OS, AS SAMTOOLS IS NOT AVAILABLE ON WINDOWS)Exercise 3: Variant Calling 1. Configure the Input File node labled (BAM alignment file) by selecting the BAM file human_hbb_gene.bam located under the provided data folder. 2. Similarly, configure the Input File node labled (Reference gene) by selecting the FASTA file human_hbb_gene.fasta located under the provided data folder. 3. Use the provided SortBAM node to sort the results. The result has to be sorted before variant calling. 4. Perform variant calling using SamtoolsMPileup node. (Hint: Connect the original Reference Genome to the optional port.) 5. The result from the previous step is a binary file in BCF format. Use BcfToVcf node to convert it to a human readable (VCF) format persist files by moving them from tmplocations to a directory of choice Variant CallerConverterSort BAMRead BAM alignment fileReference gene SamtoolsMPileup BcfToVcf SortBam Input File Input File Copy/Move Files Port to URI

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