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Robinn Teoh

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Latest activity by Robinn Teoh
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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve-Brandt-she-her Here are the outputs of the commands: 11:13:59.955 INFO FlagStat - 0 read(s) filtered by: WellformedReadFilter874579472 read(s) filtered by: ReadGroupReadFilter874579...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve-Brandt-she-her, I have tried putting in the read groups from BWA-MEM and re run the whole pipeline, and here are my answers: For #1, I found out what was the issue and it came from t...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve,  For #1 I was looking on SAM specification but they didn't specify the format, but BWA-MEM homepage showed this: complete read group header line. ’\t’ can be used in STR and will b...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve-Brandt-she-her For issue no.1: I have \t characters in my other bam files which have successful BQSRs, so I really do wonder if that is actually the main error though. When I use sam...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve-Brandt-she-her, I have edited my previous comment, and so sorry for causing the trouble! May I ask what issue that might be? Just to make a comparison I will attached the @RG for the...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve-Brandt-she-her, I am not too sure how should I be going about to investigate, but I will show you what the logs of my command exports: samtools view -H Kuu_sorted_dedup.bam > Kuuhea...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear  Genevieve, What if that is the only read group I have in my BAM file? @RG ID:PG3847_01_a LB:PG3847_01_A3535_H1 PL:Illumina PU:H753JDSXY.2 PM:Novaseq6000 SM:KuuKuu_tm_R1.fastq.gz@PG ID:bwa PN...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve, So sorry for the confusion. I will clarify the situation: I have a BAM file (A) which holds the original header for the read group, one which I performed BaseRecalibrator on which p...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve, Just to confirm, I was supposed to apply BQSR table from my previous bam file to the new reheaded bam file, yes no? As when I try to run BaseRecalibrator on my reheaded bam file i g...

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    Robinn Teoh commented,

    1. Community
    2. Germline
    3. [Repost] ReadGroup missing when Applying BQSR

    Dear Genevieve, Understood. I will retry the method which you have suggested above and get back to you when I am done with it. Thank you for your support throughout the whole conundrum! Best wishes...