Where do reads for variant calling come from (2pts)? How can variations be visua
ID: 80655 • Letter: W
Question
Where do reads for variant calling come from (2pts)? How can variations be visualized in the alignment step of variant calling (2pts)? What do different colors/shades of color represent in variant calling (2pts)? What does paired end sequencing mean in context of variant calling of NGS data? What would be difference between 4x and 30x coverage of sequencing reads? Would a 5x rage or a 10x coverage find more variations (2pts)? Which sequencing budget is ideal for finding s variations in a diseased patient (3pts)? A SAM file contains (2pts)? A BAM file contains (2pts)? A VCF file is (2pts)? How are alternative SNPs (more than one) represented in a VCF file (2pts)? What kind of role do quality scores play in variant calling (3pts)?Explanation / Answer
Answer 8& 9 :- In SAM file we contain SAM Format of data . SAM Format is a text format for storing sequence data in a series of tab delimited ASCII columns.
The BAM file contains BAM Format of data which is a binary format for storing sequence data.SAM files
can be used to store sequence data, both aligned as well as unaligned, in a human readable format.
Compare:-
BAM and SAM formats are designed to contain the same information. The SAM format is more human readable, and easier to process by conventional text based processing programs, such as awk, sed, python, cut and so on. The BAM format provides binary versions of most of the same data, and is designed to compress reasonably well.
Answer 10:- VCF stands for Virtual Contact File also called vcard which are used to store contact information for individuals and businesses in a digital file format. This files contain information related to phone number and other contact information for the person creating the file and we can store images media also.we can used to transfer contact information between address books and can also be attached to email messages. VCF files can be used on Windows and Mac operating systems and iphone
Answer 4 Paired end is better than single end or un paired data for alignment Because Paired-end reads are essentially "longer" reads, allowing the aligner to better align around repetitive regions, gaps, etc.
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