User: 543541656

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54354165620
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Posts by 543541656

<prev • 9 results • page 1 of 1 • next >
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Answer: A: java.lang.IllegalArgumentException: samples cannot be empty when i run gatk-pac
... hello,have you solved the problem?? I have the same problen as you. ...
written 10 weeks ago by 54354165620
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an error occurring after run the annovar commad ,
... perl annotate_variation.pl --geneanno --dbtype refGene --buildver msuv7 --outfile /home/riceUsers/fyx/qtl-bm4-mw/5.compare/20.awk_custom2/mut_index_2/msu_result /home/riceUsers/fyx/qtl-bm4-mw/5.compare/20.awk_custom2/mut_index_2/candidatesnp_final.avinput msudb/ NOTICE: Output files are ...
snp annotation written 5 months ago by 54354165620 • updated 5 months ago by Kevin Blighe67k
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an problem occuring when using fastq_quality_filter
... how can i sove the problem when i execute the following command?? gunzip -c 9311/9311_2.Rn.1.gz | fastq_quality_filter -Q 33 -v -q 30 -p 90 -z -o 9311/q30p90/9311_2.RnFq30p90.1.gz Segmentation fault (core dumped) ...
reads filter fastq_quality_filter written 6 months ago by 54354165620
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Answer: A: BQSR Recalibration for Mycobacterium Genome Data
... According to what the gatk forum said,you can bootstrap a database of known SNPs. Here's how it works: First do an initial round of SNP calling on your original, unrecalibrated data. Then take the SNPs that you have the highest confidence in and use that set as the database of known SNPs by feeding ...
written 7 months ago by 54354165620
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know sites of rice for BaseRecalibrator
... how can i get the know sites of the rice for BaseRecalibrator? samtools(mpileup)+bcftools? or gatk Haplotypecaller? finally i want to get the credible snps and indels from my resequence data of rice ...
dna-seq written 7 months ago by 54354165620
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is the output.table correct after BQSR?
... Hi, after I ran the BQSR command gatk --java-options "-Xmx4G" BaseRecalibrator -R /home/riceUsers/fyx/bm4/reference/1_genomic.fna -I 1_dedup.bam --known-sites 1_round1_passed_snp.vcf --known-sites 1_round1_passed_indel.vcf -O 1_round1.table my cotents of the output.table is as follows,I want ...
gatk bqsr written 7 months ago by 54354165620 • updated 7 months ago by Pierre Lindenbaum131k
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Comment: C: there is an error after samtools index
... no,I just copy someone else's code,because it is the first time to use that for me. ...
written 7 months ago by 54354165620
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Comment: C: there is an error after samtools index
... thank you,I have solved the problem according to your requirements ...
written 7 months ago by 54354165620
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there is an error after samtools index
... Hi, there is an error occuring after the following command [E::hts_idx_push] Unsorted positions on sequence #4: 27130750 followed by 27130362 samtools index: failed to create index for "1_sorted.bam" and my samtools sort command is samtools sort 1_raw.bam -n -m 2G -@ 4 -o 1_sorted.bam [bam_sor ...
dna-seq written 7 months ago by 54354165620 • updated 7 months ago by swbarnes29.1k

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