Samtools Convert Sam To Bam With Code Examples

Samtools Convert Sam To Bam With Code Examples

In this session, we’ll try our hand at solving the Samtools Convert Sam To Bam puzzle by using the computer language. The code that follows serves to illustrate this point.

# Basic syntax:
samtools view -S -b sam_file.sam > bam_file.bam
# Where:
#	-S specifies that the input is a sam file
#	-b specified that the output should be written in bam format
# To convert a bam file to a sam file, use:
samtools view -h -o sam_file.sam bam_file.bam

We were able to fix the Samtools Convert Sam To Bam problem by looking at a number of different examples.

How do I convert SAM to BAM files with samtools?

To convert SAM to BAM, we use the samtools view command. We must specify that our input is in SAM format (by default it expects BAM) using the -S option. We must also say that we want the output to be BAM (by default it produces BAM) with the -b option.20-Nov-2013

What does samtools index do?

The samtools index command creates a new index file that allows fast look-up of the data in a sorted SAM or BAM file.

How do I open a BAM file with samtools?

EXAMPLES

  • Import SAM to BAM when @SQ lines are present in the header: samtools view -bo aln.bam aln.sam If @SQ lines are absent: samtools faidx ref.fa samtools view -bt ref.fa.fai -o aln.bam aln.sam where ref.fa.fai is generated automatically by the faidx command.
  • samtools view -C -T ref.fa -o aln.cram aln.bam.

What is a sorted BAM file?

Sorted BAM has the data sorted by chromosomes/contigs/scaffolds whatever is in your reference genome. In order to efficiently display/access the data the BAM file has to be sorted. For viewing aligned/sorted BAM files use integrated genome viewer (IGV) on windows.17-Oct-2013

What does samtools Flagstat do?

DESCRIPTION. Does a full pass through the input file to calculate and print statistics to stdout. Provides counts for each of 13 categories based primarily on bit flags in the FLAG field. Information on the meaning of the flags is given in the SAM specification document <samtools.github.io/hts-specs/SAMv1.pdf&gt;.18-Aug-2022

What does samtools Fixmate do?

Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.

What is the difference between SAM and BAM files?

BAM files contain the same information as SAM files, except they are in binary file format which is not readable by humans. On the other hand, BAM files are smaller and more efficient for software to work with than SAM files, saving time and reducing costs of computation and storage.23-Nov-2021

What does it mean to index a BAM file?

Bam files can also have a companion file, called an index file. This file has the same name, suffixed with . bai. This file acts like an external table of contents, and allows programs to jump directly to specific parts of the bam file without reading through all of the sequences.

How do you convert BAM to Fastq?

Converting BAM to fastq

  • samtools sort -n SAMPLE.bam -o SAMPLE_sorted.bam.
  • samtools fastq [email protected] 8 SAMPLE_sorted.bam \
  • -1 SAMPLE_R1.fastq.gz \
  • -2 SAMPLE_R2.fastq.gz \
  • samtools bam2fq SAMPLE.
  • cat SAMPLE.fastq | grep ‘^@.*/1$’ -A 3 –no-group-separator > SAMPLE_r1.fastq.

What does samtools view do?

Samtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the formats, does sorting, merging and indexing, and can retrieve reads in any regions swiftly. Samtools is designed to work on a stream.18-Aug-2022

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