Programming/Commands Flashcards

1
Q

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

A

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

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2
Q

BAM sorting

A

samtools sort my.bam > my-sorted.bam

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3
Q

BCFTOOLS to create VCF file

A

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

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4
Q

Perform alignment

A

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

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