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Aziz

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Latest activity by Aziz
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    Aziz created a post,

    HaplotypeCaller does not work

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    REQUIRED for all errors and issues: Due to MODULEPATH changes, the following have been reloaded:  1) ImageMagick/7     7) gnuplot/4         13) pcre/8.38              19) tidyp/1.04  2) R/3.4.2    ...

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    Aziz commented,

    Hello, I used GAYK/ 3 to combine multiple vcf files in the past, but it is no longer working. GenomeAnalysisTK -at 8 -T GenotypeGVCFs  Now, I tried to use this command to combine multiple vcf files...

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    Aziz created a post,

    combine GVCF

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    REQUIRED for all errors and issues: a) GATK version used: ml biocontainers gatk4/4.2.5.0 b) Exact command used: gatk CombineGVCFs \-R persian_walnut_junglans_regia_chrs_sept18.fasta \--variant SRR1...

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    Aziz created a post,

    GVCF

    REQUIRED for all errors and issues: a) GATK version used: module load GATK/3.6.0 b) Exact command used: GenomeAnalysisTK -nt 8 -T GenotypeGVCFs \-R persian_walnut_junglans_regia_chrs_sept18.fasta \...

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    Aziz commented,

    Hi Genevieve, I want to generate vcf files from several bam files. I got this error. Would you please let me know how to fix this problem. htsjdk.samtools.SAMFormatException: Invalid GZIP header   ...