User: cmccabe

gravatar for cmccabe
cmccabe180
Reputation:
180
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Location:
Chicago
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1 month, 1 week ago
Joined:
4 years, 8 months ago
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c******@luriechildrens.org

Posts by cmccabe

<prev • 210 results • page 1 of 21 • next >
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180
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6 follow
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samtools covert to bam, sort and index all gz.sam
... The below bash script utilizes samtools in parellel to convert all gz.sam in a directory, sort, and index (I think). However, it seems to be processing a long time and I am not sure if it is indexed. Is there a better, more-efficient way? Without the .gz it is much faster. I am using samtools 1.9. T ...
parellel samtools written 6 weeks ago by cmccabe180 • updated 6 weeks ago by cmdcolin1.1k
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Comment: C: gatk vqsr --recal-file error
... Thank you very much :). ...
written 6 months ago by cmccabe180
2
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1
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379
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gatk vqsr --recal-file error
... In GATK 4.0.6.0 I am getting the below error using the command: gatk VariantRecalibrator \ -R /home/cmccabe/Desktop/fastq/resources/ucsc.hg19.fasta \ -V NA12878.vcf.gz \ --resource hapmap,known=false,training=true,truth=true,prior=15.0:/home/cmccabe/Desktop/f ...
gatk vqsr written 6 months ago by cmccabe180 • updated 6 months ago by Santosh Anand4.6k
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337
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Comment: C: error using bqsr and incompatible contigs
... Thank you both very much :). ...
written 6 months ago by cmccabe180
2
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error using bqsr and incompatible contigs
... Using the below command in GATK 4.0.6.0, I am getting: A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found. Code: gatk BaseRecalibrator \ -I NA12878_mark_duplicates.bam \ -R /home/cmccabe/Desktop/fastq/res ...
gatk bqsr written 6 months ago by cmccabe180 • updated 5 weeks ago by Biostar ♦♦ 20
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Comment: C: GATK MarkDuplicates output and bam
... So this was nextseq data with a PF of 130,580,858 and RG1 had 56,000,000 and RG2 ha 55,000,000 with the Q30 ~ 87%. Thank you :). https://basespace.illumina.com/analyses/113086485/results/140322187 ...
written 6 months ago by cmccabe180
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Comment: C: GATK MarkDuplicates output and bam
... Yea, sorry for the typo. I downloaded it from basespace, combining read group 1 and 2, aligned, and markduplicates. I have to look more into it as i am not sure the details. Thank you :). ...
written 6 months ago by cmccabe180
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Comment: C: GATK MarkDuplicates output and bam
... This is public exome data using NA1278. I will have to read up on illumina analysis, i am very new to it. So the BQSR step seems dependent on base quality, is there a particular tool to use. Currently, i am aligning with bwa-mem, markdupicates, bqsr. Maybe a qualitry step after alignment. Thank you ...
written 6 months ago by cmccabe180
2
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GATK MarkDuplicates output and bam
... The below command executes and produces the dup_metrics below, I am trying to interpret them and don't really understand the metrics and in the bam file is the PG tag MarkDuplicates a duplicate read. I am using public data and if I GATK BQSR do I need to remove the duplicates or just mark them? Than ...
gatk markduplicates written 6 months ago by cmccabe180 • updated 6 months ago by finswimmer10k
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Comment: C: multithread support for gatk
... Thank you very much :). ...
written 6 months ago by cmccabe180

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