Integration of paired and single-end SRA

Question

[reza]

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?

Answer 1

[Brian Bushnell]

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.