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- maintained as archival files. Fastq files can be regenerated from the bam files (samtools sort -n to sort bam files by read names, and converted back to fastq files...15 KB (1,174 words) - 14:40, 25 October 2023
- realigns around indels: usage: perl run_samtools_only_parental_v2.pl read_list genome SE_or_PE example: perl run_samtools_only_parental_v2.pl gwas_higher_coverage_indivs...95 KB (13,429 words) - 14:57, 26 March 2024
- put the samtools manual in there. $ mkdir -p ~/man/man1 $ cp samtools.1 ~/man/man1 $ ll ~/man/man1 Now let's try to call samtools: $ samtools Unix can’t...38 KB (5,351 words) - 11:21, 28 January 2018
- individuals per population, e.g.: 2\n1\n3\n Covert a samtools vcf file to input counts for ASE pipeline: perl samtools_vcf_to_ASE_counts.pl infile.vcf Writes an output...32 KB (4,368 words) - 15:10, 8 June 2023
- RRedon:Protocols/Variation pipeline (section samtools)'min depth': how do we use it , when ? ↓TODO samtools pileup -vcf ${HG18}.fa file.bam |\ samtools/misc/samtools.pl varFilter -d 4 -D 1200 -Q 25 d: Minimum...5 KB (600 words) - 01:58, 18 June 2010
- 23 bytes (0 words) - 20:10, 12 January 2019
- export to bam ? samtools view output.sam > output.bam ← Fix this! I used this ? Use the reference genome indexed by samtools samtools import hg18.fa.fai...1 KB (180 words) - 00:49, 9 June 2010
- MergeSamFiles.jar > $final.bam samtools sort -n $final.bam $final.nameSort samtools fixmate $final.nameSort.bam $final.fm.bam samtools sort $final.fm.bam $final...886 bytes (117 words) - 08:23, 2 June 2010
- 2 17:03 hg18.fa.rsa -rw-r--r-- 1 root root 370M jun 2 16:47 hg18.fa.sa samtools faidx hg18.fa will create a file: hg18.fa.fai...2 KB (309 words) - 08:27, 2 June 2010
- to have samtools installed and in your path. If not, do task 1 from the basic Unix tutorial before you continue. Note: it seems that the samtools view command...33 KB (4,704 words) - 07:18, 27 September 2017
- aligner. SAMtools - SAMtools. GATK - GATK at the Broad. Tablet - Tablet, visualizes ACE, AFG, MAQ, SOAP, SAM and BAM formats. SAMtools - SAMtools. BLAST...5 KB (461 words) - 13:17, 20 June 2012
- bam format use samtools: samtools view -but my_genome.fasta.fai -o reads_vs_my_genome_db.unsorted.bam reads_vs_my_genome_db.sam samtools sort reads_vs_my_genome_db...12 KB (1,677 words) - 02:50, 30 September 2014
- Standard usage: #create samtools fasta index used to insert FASTA header sequence info in SAM 2 BAM. Creates ref_genome.fa.fai samtools faidx ref_genome.fa...18 KB (3,053 words) - 01:48, 20 September 2014
- FASTQ - Wikipedia's FASTQ page. FASTA - Wikipedia's FASTA page. SAMtools - SAMtools. AMOS - AMOS. UCSC - UCSC's faq on file formats. TileQC - Requires...8 KB (647 words) - 17:46, 5 June 2012
- sorting and indexing we will use samtools: samtools sort unsorted_input.bam sorted_output #notice no bam suffix!!! samtools index sorted_output.bam #creates...25 KB (4,166 words) - 10:56, 11 September 2014
- bed module load biology module load samtools samtools depth my_bam_file | awk '{sum+=$3} END { print sum/NR}' samtools view -c -F 260 my_bam_file...3 KB (266 words) - 20:29, 12 January 2019
- nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK A more in-depth variant detection strategy based on GATK GAGE...4 KB (0 words) - 16:41, 23 September 2017
- QC FASTX toolkit Lab Home Lab Meeting Laboratory Protocols BEDtools SAMtools samtools can also be used for making pileups, calling variants, and filtering...39 KB (4,567 words) - 08:27, 22 August 2017
- individuals per population, e.g.: 2\n1\n3\n Covert a samtools vcf file to input counts for ASE pipeline: perl samtools_vcf_to_ASE_counts.pl infile.vcf Writes an output...4 KB (504 words) - 12:04, 16 November 2018
- $ID perl /home/groups/schumer/shared_bin/Lab_shared_scripts/getScaffold_samtools.pl $FASTA $CHR > "$ID"_"$CHR".fa sed -i "s|"$CHR"|"$ID":"$CHR"|g" "$ID"_"$CHR"...15 KB (2,418 words) - 13:08, 7 November 2023
