SNP calling tools
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3.9 years ago
kalyanimeha ▴ 40

Hie I am new to the NGS field. I have to calculate the Loss of Heterozygosity for which I need to calculate the SNP. In SNP , i want to check the allele frequencies specifically. SO, is there any tool available that can do this work in very less time. I used "bcftools mpileup" but it is taking too much time because I have 221 samples. So, I am in search of some tool which can do the work very fast. I also used "freebayes" but it also took too much time. Thanks in advance for your suggestions and help.

SNP next-gen • 506 views
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I am in search of some tool which can do the work very fast.

You are already using the best tools for the analyses mentioned. If you have many samples then it is going to take time to do proper analysis.

Are you taking advantage of multi-threading to start more than one threads so the tools can work faster? At the end of the day required time is going to depend on compute resources you have available and the amount of data you have.

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