checkBamHeadersđĞxit if difference in BAM headers baq 0 adjust qscores around indels (as SAMtools), supply -ref C 0 adjust mapQ for excessive mismatches (as SAMtools), supply -ref only_proper_pairsđ Only use reads where the mate could be mapped trim 0 Number of based to discard at both ends of the reads minQ 13ĝiscard bases with base quality below minMapQĐĝiscard reads with mapping quality below show 0 Mimic 'samtools mpileup' also supply -ref fasta for printing reference column uniqueOnlyĐĝiscards reads that doesn't map uniquely remove_badsđĝiscard 'bad' reads, (flag >=256) rf (null) Supply multiple regions in a file (see examples below) r (null) Supply a single region in commandline (see examples below) > Analysis helpbox/synopsis information: angsd -out out -doMaf 2 -bam bam.filelist -doMajorMinor 1 -GL 1 -P 5 Includeflag: (beta)each segment properly aligned according to the aligner,Įxample of estimating allele frequencies from bam files minChunkSizeĒ50 Minimum size of chunk sent to analysesĬhr:start- Use region from start to end of chrĬhr:-stop Use region from beginning of chromosome: chr to stopĬhr:start-stop Use region from start to stop from chromosome: chrĬhr:site Use single site on chromosome: chr downSampleĐ.000000ĝownsample to the fraction of original data doCheckđ Keep going even if datafile is not suffixed with.
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The filelist is a file containing the full path for each bam file with one filename per row. home/software/angsd/test/smallBam/smallNA12761.bam home/software/angsd/test/smallBam/smallNA11993.bam home/software/angsd/test/smallBam/smallNA06985.bam home/software/angsd/test/smallBam/smallNA12004.bam home/software/angsd/test/smallBam/smallNA11830.bam home/software/angsd/test/smallBam/smallNA12763.bam #.bam file format full Specify multiple regions in a file using the same syntax as -r Specify a region with in a chromosome using the syntax. Same as the samtools flags -x which removes read with a flag above 255 (not primary, failure and duplicate reads). Remove reads that have multiple best hits. Number of bases to remove from both ends of the read.
Include only proper pairs (pairs of read with both mates mapped correctly).
1: include only proper (default), 0: use all reads. Only relevant for paired end data.Īdjust mapQ for excessive mismatches (as SAMtools), supply -ref. Perform BAQ computation, remember to cite the | BAQ paper for this.ġ:normal BAQ (same as default in SAMtools).Ģ:extended BAQ (same as default in SAMtools). If zero then it will use the existing record Not performing this check is not advisable You will need to supply your reference (-ref) for BAQ options.Įxits if the headers are not compatible for all files. Minimum number of sites to read in before starting to analyze - larger number will use more RAM 0.25 will on average keep 25% of the reads Randomly remove reads to downsample your data. Pileup files are the output files that are generated by SAMtools mpileup. angsd -pileup sam.mpileup -nInd 10 -fai hg19.fa.gz.fai -domaf 1 -domajorminor 1 -gl 1īCF/VCF file as input is now included but with some limitations. Only chr,pos and PL tags are being used, and we discard indels.
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