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Example vcf (4.0) excerpt:
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CHR POS ID REF ALT
10 414931 S10_414931 A G
10 429671 S10_429671 A -
10 429672 S10_429672 T -
10 429673 S10_429673 A -
10 429674 S10_429674 T -
10 429713 S10_429713 C G
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As you can see sites xx671-674 are all just one indel. I would like to merge these four indels into one. What is the best way to accomplish this?
Note that "bcftools filter -G" doesn't recognize any of these sites as indels.
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CHR POS ID REF ALT
10 414931 S10_414931 A G
10 429671 S10_429671 A -
10 429672 S10_429672 T -
10 429673 S10_429673 A -
10 429674 S10_429674 T -
10 429713 S10_429713 C G
-------------------------------------------------
As you can see sites xx671-674 are all just one indel. I would like to merge these four indels into one. What is the best way to accomplish this?
Note that "bcftools filter -G" doesn't recognize any of these sites as indels.