merge nearby variants in vcf from mutect2

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Junfeng Jiang

• August 12, 2021 14:36
• Edited

Hi all,

Is there any method that can combine/merge variants nearby into a new variant

For example, three variants listed as follows can be merged to new one: EGFR c.2237_2253delinsTG p.E746_T751delinsV

7 55242466 . GAA G clustered_events 0.00143 EGFR:NM_005228:exon19:c.2237_2238del:p.E746Vfs*16

7 55242473 . GAGAAGCAACA G clustered_events 0.00142 EGFR:NM_005228:exon19:c.2244_2253del:p.R748Sfs*15

7 55242469 . TTAA T clustered_events 0.00142 EGFR:NM_005228:exon19:c.2240_2242del:p.L747_A1210del

Any method that can process such variants?

 

Thanks,

Junfeng

 

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  Pamela Bretscher

  • August 16, 2021 17:07

  Hi Junfeng Jiang,

  Have you verified that these variants are from the same sample and are phased properly? I'm not sure why the tool would output three separate deletions that are all in a row when it could output one deletion. If everything has been done properly, then I don't believe there is a GATK tool that would achieve what you are looking for.

  Kind regards,

  Pamela

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