Programming/Commands

Question 1

BAM format is the binary version of a SAM file. The conversion can be performed using samtools:

Answer 1

samtools view -S -b my.sam > my.bam

Question 2

BAM sorting

Answer 2

samtools sort my.bam > my-sorted.bam

Question 3

BCFTOOLS to create VCF file

Answer 3

bcftools mpileup –fasta-ref reference_chr10_chr18.fa sorted.bam > sorted.vcf

Question 4

Perform alignment

Answer 4

mkdir path_to_folder_where_BWA_index_will_be_created
bwa index -p path_to_folder_where_BWA_index_will_be_created path_to_reference_sequence/reference_chr10_chr18.fa
bwa mem path_to_folder_where_BWA_index_has_been_created path_to_reads_file/mate_1.fq path_to_reads_file/mate_2.fq > path_to_place_results/results.sam