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3. DP for each variant bulk is skewed towards 50 and multiples of 50

The expected depth of coverage is 40 for my samples.

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• Lauren Fedenia
• April 23, 2021 21:09
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1. Community
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3. DP for each variant bulk is skewed towards 50 and multiples of 50

java -jar picard.jar FastqToSam F1=Red_sorghum_bulk_FseI_130bp_seqs.txt.trimmed_seqs.fastq O=red-bulk_unaligned_reads.bam READ_GROUP_NAME=@D00572.1 SAMPLE_NAME=RedBulk LIBRARY_NAME=Illumina-111111 ...

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• Lauren Fedenia
• April 23, 2021 13:57
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1. Community
2. New User Advice
3. DP for each variant bulk is skewed towards 50 and multiples of 50

Genevieve,   Yes, we are concatenating 70 fastq files/samples per bulk pool to perform variant calling on.  When I we analyze the depth and coverage outside of the GATK pipeline, we do not obtain a...

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• Lauren Fedenia
• April 22, 2021 21:15
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