Changes

! Description

! Description

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|-  

|style=white-space:nowrap|<code>--in <file></code>

|style=white-space:nowrap|<code>--in <filename></code>

| Input VCF file. The latest 1000 Genomes files can be found [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel here]

| Input VCF file. The latest 1000 Genomes files can be found [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel here].

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|-  

| <code>--out <file></code>

| <code>--out <filename></code>

| Output VCF filename

| Output VCF filename.

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|-

| <code>--states 200</code>

| <code>--uncompress</code>

| Number of haplotypes to consider during each update. Increasing this value will typically lead to better haplotypes, but can dramatically increase computing time and memory use. A value of 200 - 400 is typical.  

| write an uncompressed VCF output file.

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| <code>--rounds 20</code>

| <code>--sampleSubset <filename></code>

| Iterations of the Markov sampler to use for haplotyping. Typically, using 20 - 30 rounds should give good results. To obtain better results, it is usually better to increase the <code>--states</code> parameter.

| <code>--filterList <filename></code>

| filename of file containing regions to include. <br>format: start end <br> start & end positions should be 1-based inclusive positions.

| <code>--params</code>

| print the parameter settings

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[[Category:Software]]

[[Category:Software]]