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Integration of paired and single-end SRA

Hi

Can I conduct a genomic data analysis project using the integration of paired-end and single-end data for variant identification, as well as for detecting selection signatures, introgression?

Can the methods and programs used in a resequencing data analysis using paired or single- end datat also be applied in this approach? In other words, can I perform all the analyses in a similar way on both types of data and ultimately use GATK to create a final VCF file?

paired-end single-end vcf resequencing
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updated by Brian Bushnell Brian Bushnell • written by reza reza

1 answer

I don't know how GATK will react, but in principle there's no problem. For BBTools, at least, more coverage is always better when doing variant-calling, even if the additional coverage is single-ended. That's probably true for GATK as well.

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written by Brian Bushnell Brian Bushnell

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