Hanan Sela
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Activity overview
Latest activity by Hanan Sela-
Hanan Sela commented,
Hello Can I use GVCF file generated with --create-output-variant-index = false in downstream applications such as GenomicsDBImport and GenotypeGVCFs? Is SAMtools or BCFtools generated CSI of GV...
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Hanan Sela commented,
Hi In this post it is claimed that indexing with samtools after GVCF generation can help. Is SAMtools generated CSI is compatible with downstream applications such as GenomicsDBImport and Genoty...
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Hanan Sela created a post,
java.lang.ArrayIndexOutOfBoundsException: Index 32770 out of bounds for length 32770
REQUIRED for all errors and issues: a) GATK version used:atk-4.4.0.0 b) Exact command used: ~/gatk-4.4.0.0/gatk --java-options "-Xmx100g" HaplotypeCaller -R ~/SVEVO.fas -I SAMP.bam -O SAMP.g.vcf.g...
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Hanan Sela commented,
Hello, I did as suggested and split the bam file to less than 512Mbp so it can be indexed with bai file. I still get the 32770 error. The ref.fatsa (10GB) indexing with dictionary and fai was not ...