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I figured out where the problem was. Since we have Isaac aligned bam files we use RevertSam to unalign the bam files. This was also the point where the problem was introduced. I wanted to use the options REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALI…
That was a typical case of need more coffee/ need to get some sleep: It should mention: After MergeBamAlignment and MarkDuplicates (instead of twice MarkDuplicates) I am using a object store to save the intermediate results. The files are copied t…
First of all , thanks for the time and effort you spend on this topic. I ran a small sample to save some time: the errors are the same, only another chromosome The reads after bwa mem: bam header @SQ SN:chr9 LN:138394717 The reads D0KU2ACX…
I will rerun this sample and extract the unwilling reads.
(Quote) The source was a Isaac aligned file which has been unaligned by RevertSam | MarkIlluminaAdapters. the options for RevertSam were: OUTPUT_BY_READGROUP_FILE_FORMAT=bam \OUTPUT_BY_READGROUP=true \SANITIZE=true \MAX_DISCARD_FRACTION=0.005 \ATTR…
(Quote) I do save all commands executed in a database and it does use b38/hg20 reference (Quote) I added this using MergeBamAlignment PROGRAM_GROUP* options This error occur 210 times for a full size GIAB sample
The feature request can be found at https://github.com/broadinstitute/picard/issues/645
@Geraldine_VdAuwera I will put a feature request at the Picard github repo. I will post the link to the feature request when I made the request.
No, it does not: it gives the following output: When OUTPUT_BY_READGROUP=true and OUTPUT is provided, it must be a directory: revertsam.bam Which is in line with the documentation.
I'm using picard 2.60: The command's I ran are: mkdir revertsam java -jar picard.jar RevertSam TMP_DIR=. I=sample.cram OUTPUT_BY_READGROUP=true SORT_ORDER=queryname O=revertsam COMPRESSION_LEVEL=1 REFERENCE_SEQUENCE=ref.fasta Because the input is …