Lauren Fedenia
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Activity overview
Latest activity by Lauren Fedenia-
Lauren Fedenia commented,
The expected depth of coverage is 40 for my samples.
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Lauren Fedenia commented,
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 commented,
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 created a post,
DP for each variant bulk is skewed towards 50 and multiples of 50
When using the GATK pipeline to call variants, I end up obtaining a DP for each variant skewed towards 50 and multiples of 50 (see photo below) when my average read depth from my sequencing files ...
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Lauren Fedenia created a post,
Paired-End Reads and Variant Calling
I am trying to call variants from paired-read whole genome reseq data. I have two fastq files (forward and reverse) for each sample. I got to the MergeBamAlignment command and no matter what I tr...
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Lauren Fedenia created a post,
How do I input two separate paired-end fastq files into the GATK pipeline? Do I use an interleave-fastq?
AnsweredCan you please provide a) GATK version used 4.0.3.0 b) Exact GATK commands used c) The entire error log if applicable.