Finding Snps From A Bam File

Question

[Varun Gupta]

Hi everyone

I have dna seq dataset for S.cerevisiae genome. I have aligned bam files and the ref seq genome. I would like to know some methods for finding snps from the bam files as input.

I know 2 ways to do it.

1. Using samtools mpileup and then bcftools and generating a vcf file.

2. Using GATK unified Genotyper

Any other method if you could tell would be really nice

Hope to hear from you soon

Regards

Varun

Answer 1

[Gabriel R.]

This question has been addressed before : What methods do you use for In/Del/SNP calling?

[Ashutosh Pandey]

You pasted it before me. You won. :-)

Answer 2

[Ashutosh Pandey]

There are many tools for finding SNPs but the ones you mentioned are the most used or popular ones. So if I would be in your place I will just use those tools (samtools and GATK). I used them to call SNPs for a particular strain and found 95% of the SNP calls in common.

One of the many posts (search for 'SNP calling' on bistars.org) that discuss the snp calling

What methods do you use for In/Del/SNP calling?

Answer 3

[Pierre Lindenbaum]

Ok let's have fun with the semanticmedia wiki interface of http://seqanswers.com

The semantic data of the wki can be downloaded from

http://seqanswers.com/wiki/Special:ViewXML?title=Special%3AViewXML&categories%5BBioinformatics_application%5D=on

the following stylesheet extracts the application having input=BAM and output=VCF

<xsl:stylesheet xmlns:xsl="&lt;a href="http://www.w3.org/1999/XSL/Transform" "="" rel="nofollow">http://www.w3.org/1999/XSL/Transform'
xmlns:str="http://exslt.org/strings"
extension-element-prefixes="str"
version='1.1'
>

<xsl:output method="text"/>
<xsl:template match="/">
<xsl:apply-templates select="/Pages/Category/Page/Template[@Name='Bioinformatics_application']"/>
</xsl:template>

<xsl:template match="Template">
<xsl:variable name="pageName" select="../@Title"/>
<xsl:variable name="input" select="Field[@Name='input format']"/>
<xsl:variable name="output" select="Field[@Name='output format']"/>
<xsl:for-each select="str:tokenize($input,', ')">
<xsl:if test="./text()='BAM'">
<xsl:for-each select="str:tokenize($output,', ')">
<xsl:if test="normalize-space(./text())='VCF'">
<xsl:text>http://seqanswers.com/wiki/</xsl:text>
<xsl:value-of select="$pageName"/><xsl:text>
</xsl:text>
</xsl:if>
</xsl:for-each>
</xsl:if>
</xsl:for-each>
</xsl:template>

</xsl:stylesheet>

result:

$ xsltproc stylesheet.xsl   "http://seqanswers.com/wiki/Special:ViewXML?title=Special%3AViewXML&categories%5BBioinformatics_application%5D=on"

• http://seqanswers.com/wiki/SAMtools
• http://seqanswers.com/wiki/BEDTools
• http://seqanswers.com/wiki/Atlas_Suite
• http://seqanswers.com/wiki/Dindel
• http://seqanswers.com/wiki/Freebayes
• http://seqanswers.com/wiki/RTG_Investigator
• http://seqanswers.com/wiki/Pybedtools
• http://seqanswers.com/wiki/Ngs-pipeline
• http://seqanswers.com/wiki/Contra
• http://seqanswers.com/wiki/Bis-SNP
• http://seqanswers.com/wiki/Strelka

(BTW I don't know well SMW , does anyone know if it's possible to query the RDF data directly from the wiki ? is there a SPARQL point ?)