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Bair, let us know what differences you find when running samtools (0.1.10) mpileup instead of regular pileup. -
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thank you lh3,
samtools pileup updated, samtools.pl seems not changed.
I'm running the new version, hope there is no big difference for snp calling since validation has done. Will focus on small size indel (<4 bp)Leave a comment:
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samtools for indel
Hello all,
I used samtools to detect indel (aligned by bwa), which identified >1m indels, it's too much comparing with data in publications. Default setting used expect Q50.
The number of indel will drop sharply when RMS>50, the default setting is 10.
Does anyone know how to set the filter to get a reasonable number of indel? How do I know the maxmum length of indel? (bwa sampe does not have such option)
Many thanks!
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Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...03-21-2023, 01:49 PM -
Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...03-10-2023, 05:31 AM
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