Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • AnalyzeCovariates in GATK4.2

    Hi, does anyone use AnalyzeCovariates under GATK4.2.0.0? It seems that we should be able to perform BaseRecalibrator twice to get the -before and -after "recal_data.table" files and compare using AnalyzeCovariates. However, when I tried the following commands,

    ----------------------------------------------------------------------------------------------------------------
    # First BQSR (Already done)
    # java -jar ${RJLJ}/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \
    # BaseRecalibrator \
    # -R ${CKXLhg38} \
    # -I ${ZLJ}/6_DedupedBam/${Takara_ID}_${Sample_Name}_aligned_fixmated_sorted_deduped.bam \
    # --known-sites ${GATKFiles}/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
    # --known-sites ${GATKFiles}/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
    # --known-sites ${GATKFiles}/bundle/hg38/dbsnp_146.hg38.vcf.gz \
    # -O ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.table

    # Second BQSR
    java -jar ${RJLJ}/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \
    BaseRecalibrator \
    -R ${CKXLhg38} \
    -I ${ZLJ}/6_DedupedBam/${Takara_ID}_${Sample_Name}_aligned_fixmated_sorted_deduped.bam \
    --known-sites ${GATKFiles}/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
    --known-sites ${GATKFiles}/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
    --known-sites ${GATKFiles}/bundle/hg38/dbsnp_146.hg38.vcf.gz \
    -bqsr ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.table*\
    -O ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.after.table
    ---------------------------------------------------------------------------------------------------------------------------------------------------------------

    I got an error saying that

    ***********************************************************************

    A USER ERROR has occurred: -bqsr is not a recognized option

    ***********************************************************************

    So how can I get the -after "recal_data.table" file? Or is there any other method to perform quality check for bam files before going to variant calling?
    Thanks in advance!
    Last edited by greekkey; 08-17-2021, 12:31 AM.

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
31 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
32 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Working...
X