AswinSSoman/Variant Calling Lambda phage.md

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BWA allignment of Lambda phage genome

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Variant Calling Lambda phage.md

1. Install Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.
Download samtools-1.9, bcftools-1.9, htslib-1.9 from htslib.org
First install htslib-1.9
Unzip & go inside htslib folder in terminal and type the following.
```
./configure
 make
 sudo make install
```
Install samtools-1.9 & bcftools-1.9 using the same commands.

👉 Note:

If there are broken packages in the system like Albacore, it wont allow you to install new packages.
So force remove those packages using this link here.

2. Convert SAM to BAM

To do anything meaningful with alignment data:
- first convert the SAM to its binary counterpart, BAM format using:
```
  samtools view -b lambda.sam > lambda.bam
```
-b = output format in BAM

3. Sort the BAM

Current aligners produce alignments in random order with respect to their position in the reference genome.
It must be sorted such that the alignments occur in genome order, using:
```
      samtools sort lambda.bam -o lambda.sorted.bam
```
-o = output file

4. index the sorted BAM

Indexing is done to quickly query or extract alignments.
```
       `samtools index lambda.sorted.bam`
```

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