kostas alexiou
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Latest activity by kostas alexiou-
kostas alexiou commented,
I have managed to solve the problem of the truncated file. After all, the reheading was not working because there were reads whose mate was mapping to a different chromosome/scaffold and that this ...
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kostas alexiou commented,
Hi Genevieve Brandt (she/her). Sorry. I was not very clear in my message. My question was why I am getting a truncated bam file, after running the ReplaceSamHeader tool from picard. As you have sug...
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kostas alexiou created a post,
Truncated bam file after running ReplaceSamHeader(Picard)
AnsweredHi guys, I want to modify the header of a bam file, in order to remove all the un-anchored scaffolds, and following the steps below: 1. get the modified header from the input bam file samtools view...
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kostas alexiou commented,
Hi Bhanu, The behaviour is seen only in the GenotypeGVCFs output. I have to mention also that, in v4.1.3.0, even though the AD field is absent in the HaplotypeCaller output, when an alternative all...
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kostas alexiou created a post,
AD field presence
Hi, I have used gatk v4.1.6.0 and run the following command in order to generate the VCF file for 82 samples, after having generated first gVCF files per sample. ./software/gatk-4.1.6.0/gatk Genoty...