We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
?insert size =1
Hello, I have a batch of 170 custom designed target capture panel of 7Mb and sequenced with Illumina. I generated unmapped BAM and followed GATK best practice, similar to the GATK GitHub page. About 30 of my samples, the Picard CollectMultipleMetrics insert size shows insert size of 1. (Details of the output is attached below) In IGV, the insert size is shown as -1 to 1. The rest of the samples are normal and the problem persists despite I repeat the pre-processing once again. May I know how to troubleshoot? Thanks a lot in advance!
## htsjdk.samtools.metrics.StringHeader # CollectMultipleMetrics INPUT=/home/nelson/OPERATION/RedCellNGS/final_output/RBCWorkflow/1e670026-c28f-4d2c-8711-68a4e8ca19b4/call-GatherSortedBamFiles/execution/17H029354-5.bam ASSUME_SORTED=true OUTPUT=temp METRIC_ACCUMULATION_LEVEL=[LIBRARY, SAMPLE] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, CollectSequencingArtifactMetrics, QualityScoreDistribution] REFERENCE_SEQUENCE=/home/nelson/OPERATION/RedCellNGS/ref/Homo_sapiens_assembly38.fasta STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Wed May 08 23:36:41 HKT 2019 ## METRICS CLASS picard.analysis.InsertSizeMetrics MEDIAN_INSERT_SIZE MODE_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_95_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP 1 1 0 1 162893586 1 0 1028274 TANDEM 1 1 1 1 1 1 1 1 1 1 1 17H029354-5 1 1 0 1 162893586 1 0 1028274 TANDEM 1 1 1 1 1 1 1 1 1 1 1 17H029354-5 REDCELLNGS ## HISTOGRAM java.lang.Integer insert_size 17H029354-5.tandem_count REDCELLNGS.tandem_count 1 1020702 1020702