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3. GenotypeGVCFs and the death of the dot (obsolete as of GATK 4.6.0.0)

This feature will change the internal AF isn't it ?

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• Yokofakun
• February 06, 2024 16:51
• 1 vote

1. Community
2. Germline
3. Haplotype Caller (4.1.6.0) : java.lang.IllegalStateException: Smith-Waterman alignment failure.

Furthemore, I uploaded a minimal BAM with the error in the corresponding github issue: https://github.com/broadinstitute/gatk/issues/6490#issuecomment-605617217

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• Yokofakun
• March 29, 2020 10:48
• 0 votes

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3. Custom ReadFilter to ignore malformed reads ?

oh, I see this https://github.com/broadinstitute/gatk/pull/6498  and https://gatk.broadinstitute.org/hc/en-us/community/posts/360057963511-HaplotypeCaller-error-Read-is-malformed-read-starts-with-d...

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• Yokofakun
• March 21, 2020 13:29
• 0 votes

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3. CombineGVCFs 4.1.2.0 throws "java.lang.IllegalArgumentException: Features added out of order:"

ok, I see, thanks.

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• Yokofakun
• March 20, 2020 17:36
• 0 votes

1. Community
2. Germline
3. CombineGVCFs 4.1.2.0 throws "java.lang.IllegalArgumentException: Features added out of order:"

Hi Bhanu, thank you for your answer   > Try to upgrade to the latest version of GATK4.1.5.0 and let me know if the issue persists. I upgraded and I've got an error (I'm not testing the very same in...

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• Yokofakun
• March 19, 2020 13:28
• Edited
• 0 votes