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Juan Pablo Aguilar Cabezas

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Latest activity by Juan Pablo Aguilar Cabezas
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    Juan Pablo Aguilar Cabezas commented,

    1. Community
    2. Non-Human
    3. Error Creatting Dictionary for genome

    Hi I am running a similar problem. I bisulfite-sequenced some samples and then I called variants with sorted-bam files created with bwa-meth and with bismark and variants called with cgmaptools. Si...

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    Juan Pablo Aguilar Cabezas commented,

    1. Community
    2. Other
    3. GenomicsDBImport: Attempting to genotype more than 50 alleles

    Genevieve Brandt (she/her) You are welcome! Yes, I know that it is not an error but since I am doing demographic inference, and those sites will be skipped, right? Then, I will have less SNPs and v...

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    Juan Pablo Aguilar Cabezas commented,

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    3. GenomicsDBImport: Attempting to genotype more than 50 alleles

    Sorry the command is: singularity exec /users/PHS0338/jpac1984/appz/gatk_latest.sif gatk --java-options "-Xmx145g" GenotypeGVCFs \   -R myse-hapog.fasta \   -V combine.8-03.vcf.gz \   -O gvcf.8-03....

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    Juan Pablo Aguilar Cabezas commented,

    1. Community
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    3. GenomicsDBImport: Attempting to genotype more than 50 alleles

    Hi, my GATK version is v4.2.6.1Everything goes normal at the beginning... 06:32:00.602 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.6.1-local.jar!/...

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    Juan Pablo Aguilar Cabezas commented,

    1. Community
    2. Other
    3. GenomicsDBImport: Attempting to genotype more than 50 alleles

    Hi, I am in the same position. Not as many samples as Nils, but I have 37 samples that I put together with CombineGVCFs, and got the error message of more than 50 alleles when trying GenotypeGVCFs....

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    Juan Pablo Aguilar Cabezas created a post,

    Variant Filtering problem after merging

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    1. Community
    2. General Discussion

    REQUIRED for all errors and issues: a) GATK version used: 4.2.6.1b) Exact command used: java -jar picard.jar MergeVcfs  \          I=PA_113_DP.vcf.gz \          I=No_Pa90-16_DP.vcf.gz \          O=...

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    Juan Pablo Aguilar Cabezas created a post,

    GATK4.2.0.0 docker - Haplotypecaller optimization - how to activate Samtools asynchronous read/write

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    1. Community
    2. General Discussion

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: Docker 4.2.0.0.b) Exact command used:singularity exec gatk_latest.sif \gatk --java-options "-DGATK_STACKTRACE_ON_USER_EX...

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    Juan Pablo Aguilar Cabezas commented,

    1. Community
    2. Non-Human
    3. emit-ref-confidence error

    Genevieve Brandt (she/her) Do you know how to add it for the mapping step?I am trying the AddOrReplaceReadGroups (Picard) but since there is no multi-threading option it for one sample it is taking...

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    Juan Pablo Aguilar Cabezas commented,

    1. Community
    2. Non-Human
    3. emit-ref-confidence error

    Hi, I am having the same issue, I found that I needed to add the @RG read group information but I am trying and I have found that some of the documents provide incomplete information. For example, ...

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    Juan Pablo Aguilar Cabezas created a post,

    Variant calling/ genotyping with a chromosome-scale genome assembly

    1. Community
    2. General Discussion

    Hi, Hope you are having a great day. I am interested in conservation genomics and estimating recent demographic trends and long-runs-of-homozygosity.For this, I built a genome assembly using a refe...

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